Biocatalysts and methods for the synthesis of (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine

ABSTRACT

The disclosure provides transaminase polypeptides capable of converting the substrate, 2-(3,4-dimethoxyphenethoxy)cyclohexanone to the trans diastereomer product (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine in at least a 2:1 diastereomeric ratio relative to the cis diastereomer (1R,2S)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine. The disclosure also provides polynucleotides, vectors, host cells, and methods of making and using the transaminase polypeptides in processes for preparing (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine and its analogs, which can product compounds can be further used to prepare the aminocyclohexylether compound, (3R)-1-[(1R,2R)-2-[2-(3,4-dimethoxyphenyl)ethoxy]cyclohexyl]pyrrolidin-3-ol, which is an ion channel blocker.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a national stage application filed under 35 USC §371 and claims priority of the international application PCT/US2011/046932, filed Aug. 8, 2011, and U.S. provisional patent applications 61/510,256, filed Jul. 21, 2011, and 61/374,079, filed Aug. 16, 2010, each of which is hereby incorporated by reference herein.

1. TECHNICAL FIELD

The disclosure relates to biocatalysts and processes using the biocatalysts for the preparation of the compound (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine in enantiomeric and diastereomeric excess.

2. REFERENCE TO SEQUENCE LISTING, TABLE OR COMPUTER PROGRAM

The official copy of the Sequence Listing is submitted concurrently with the specification as an ASCII formatted text file via EFS-Web, with a file name of “CX2-053WO1_ST25.txt”, a creation date of Aug. 8, 2011, and a size of 456,034 bytes. The Sequence Listing filed via EFS-Web is part of the specification and is incorporated in its entirety by reference herein.

3. BACKGROUND

Arrhythmia is a variation from the normal rhythm of the heart beat and generally represents the end product of abnormal ion-channel structure, number or function. Both atrial arrhythmias and ventricular arrhythmias are known. The major cause of fatalities due to cardiac arrhythmias is the subtype of ventricular arrhythmias known as ventricular fibrillation (VF). Atrial fibrillation (AF) is the most common arrhythmia seen in clinical practice and is a cause of morbidity in many individuals (see e.g., Pritchett, E. L., N. Engl. J. Med. 327(14):1031 Oct. 1, 1992, discussion 1031-2; Kannel and Wolf, Am. Heart J. 123(1):264-7 Jan. 1992). Its prevalence is likely to increase as the population ages and it is estimated that 3-5% of patients over the age of 60 years have AF (see e.g., Kannel et al., N. Engl. J. Med. 306(17):1018-22, 1982; Wolf et al., Stroke 22(8):983-8, 1991). While AF is rarely fatal, it can impair cardiac function and is a major cause of stroke (see e.g., Hinton et al., American Journal of Cardiology 40(4):509-13, 1977; Wolf et al., Archives of Internal Medicine 147(9):1561-4, 1987; Wolf P. A., Abbot R D., Kannel W. B. Stroke. 22(8):983-8, 1991; Cabin R. S., Clubb K. S., Rall C., Perlmutter R A., Feinstein A. R, American Journal of Cardiology 65(16): 1112-6, 1990).

Antiarrhythmic agents have been developed to prevent or alleviate cardiac arrhythmia. PCT Publ. No. WO95/08544 discloses a class of aminocyclohexyl ester compounds as useful for the treatment of arrhythmias. PCT Publ. No. WO93/19056 discloses a class of aminocyclohexyl amides as useful in the treatment of arrhythmia and in the inducement of local anesthesia. PCT Publ. Nos. WO99/50225 and WO04/099137 disclose aminocyclohexyl ether compounds as being useful for the treatment of arrhythmias. PCT Publ. Nos. WO06/138673 and WO06/88525 describe processes for preparing aminocyclohexyl ether compounds. The aminocyclohexyl ether compound, (3R)-1-[(1R,2R)-2-[2-(3,4-dimethoxyphenyl)ethoxy]cyclohexyl]pyrrolidin-3-ol (depicted herein as compound (3)) is an ion channel blocker useful for the treatment of atrial fibrillation (see e.g., U.S. Pat. Nos. 7,057,053, and 7,259,184).

Transaminases, also known as aminotransferases, catalyze the transfer of an amino group, a pair of electrons, and a proton from a primary amine of an amino donor substrate to the carbonyl group (i.e., a keto group) of an amino acceptor molecule. Transaminases have been identified from various organisms, such as Alcaligenes denitrificans, Arthrobacter, Bordetella bronchiseptica, Bordetella parapertussis, Brucella melitensis, Burkholderia malle, Burkholderia pseudomallei, Chromobacterium violaceum, Oceanicola granulosus HTCC2516, Oceanobacter sp. RED65, Oceanospirillum sp. MED92, Pseudomonas putida, Ralstonia solanacearum, Rhizobium meliloti, Rhizobium sp. (strain NGR234), Bacillus thuringensis, Vibrio fluvialis, and Klebsiella pneumoniae (see e.g., Shin et al., 2001, Biosci. Biotechnol, Biochem. 65:1782-1788).

The stereoselectivity of transaminases in the conversion of a ketone to the corresponding amine make these enzymes useful in the asymmetric synthesis of optically pure amines from the corresponding keto compounds (see, e.g., Höhne et al., Biocatalytic Routes to Optically Active Amines,” Chem. Cat. Chem. 1(1):42-51; Zua and Hua, 2009, Biotechnol J. 4(10):1420-31). Transaminases can also be applied to the chiral resolution of racemic amines by exploiting the ability of the transaminases to carry out the reverse reaction in a stereospecific manner, i.e., preferential conversion of one enantiomer to the corresponding ketone, thereby resulting in a mixture enriched in the other enantiomer (see, e.g., Koselewski et al., 2009, Org. Lett. 11(21):4810-2).

Both R-selective and S-selective transaminases are known. The wild-type transaminase from Arthrobacter sp. KNK168 is an R-selective pyridoxal 5′-phosphate (PLP)-dependent enzyme that produces R-amines from some substrates (see e.g., Iwasaki et al., Appl. Microbiol. Biotechnol., 2006, 69: 499-505, U.S. Pat. No. 7,169,592). U.S. application Ser. No. 12/714,397, filed Feb. 26, 2010 and International application PCT/US2010/025685, filed Feb. 26, 2010, disclose engineered transaminase polypeptides derived from the naturally occurring transaminase of Arthrobacter sp. KNK168 that have increased stability to temperature and/or organic solvent, and which have been adapted to have enzymatic activity towards structurally different amino acceptor molecules (see also e.g., Savile, et al., 2010, “Biocatalytic asymmetric synthesis of chiral amines from ketones applied to sitagliptin manufacture,” Science 329(5989): 305-9).

There is a need for improved biocatalysts that can be used to prepare chiral amine intermediate compounds useful for making aminocyclohexylether compounds and new processes employing those biocatalysts that are simple, cost effective, non-hazardous, and commercially viable.

4. SUMMARY

The present disclosure provides engineered polypeptides having transaminase activity, polynucleotides encoding the polypeptides, methods of the making the polypeptides, and methods of using the polypeptides for the biocatalytic conversion of the ketone substrate of compound (1a), (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone, to the trans amine product compound (2a), (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine as shown in Scheme 1.

The (1R,2R)-trans amine product of compound (2a) is desirable as an intermediate compound for use in processes for making the active pharmaceutical agent of compound (3) (IUPAC name: (3R)-1-[(1R,2R)-2-[2-(3,4-dimethoxyphenyl)ethoxyl]cyclohexyl]pyrrolidin-3-ol).

The ketone substrate of compound (1a), however, typically is present in a mixture with the opposite enantiomer of compound (1b), (S)-2-(3,4-dimethoxyphenethoxy)cyclohexanone. Compound (1a) and compound (1b) undergo an epimerization reaction that provides an equilibrium between these two enantiomers. As shown in Scheme 2, depending on the stereoselectivity of the biocatalyst used in a transamination reaction, four different diastereomeric products can be formed from the mixture of compound (1a) and (1b): two trans amine products, compounds (2a) and (2d), and two cis amine products, compounds (2b) and (2c).

The present disclosure provides engineered transaminase polypeptides which exhibit high stereoselectivity for the R-amine products of compound (2a) and (1R,2S)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound (2c)) relative to the corresponding S-amine products of (1S,2S)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound (2d)) and (1S,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound (2b)), respectively, converting a racemic mixture of compound (1) to the R-amine products in an enantiomeric excess of at least 85% e.e., 90% e.e., 95% e.e., 98% e.e., 99% e.e., or more. Additionally, the engineered transaminase polypeptides exhibit diastereoselectivity for the trans R-amine product and are capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, as shown in Scheme 3.

Diastereomeric ratio [(2a)]:[(2c)]≧2:1

The engineered transaminase polypeptides of the present disclosure capable of converting a racemic mixture of compound (1) to the R-amine products of compound (2a) and compound (2c) in at least 98% e.e. relative to the corresponding S-amine products of compound (2d) and (2b), respectively, and producing compound (2a) in at least a 2:1 diastereomeric ratio relative to compound (2c) are synthetic variants of a naturally occurring transaminase of Arthrobacter sp. KNK168 (polypeptide of SEQ ID NO: 2), and comprise amino acid sequences that have one or more residue differences as compared to the wild-type sequence or a reference sequence of SEQ ID NO:6. The residue differences occur at residue positions that affect functional properties of the enzyme including stereoselectivity, substrate and/or product binding (e.g., resistance to substrate and/or product inhibition), activity (e.g., percent conversion of substrate to product), thermostability, solvent stability, expression, or various combinations thereof.

Accordingly, in some embodiments, engineered transaminase polypeptides of the present disclosure comprise amino acid sequences having at least 80% sequence identity to the reference polypeptide of SEQ ID NO: 6 and having amino acid residue differences as compared to SEQ ID NO: 6 at one or more of the following positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. In some embodiments, the amino acid residue differences as compared to SEQ ID NO: 6 are selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X69C; X69V; X69W; X94L; X99L; X108V; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X135Q; X136W; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I. In some embodiments, the engineered transaminase polypeptide amino acid sequences comprise one or more combinations of amino acid differences as compared to SEQ ID NO: 6 selected from the following: (a) X124V, and X210S; (b) X124V, X136W, and X210S; (c) X69V, and X136W; (d) X69V, and X215Y; (e) X69V, and X217S; (f) X69V, X124I, and X136W; (g) X69V; X136W, and X257F; (h) X44V, and X223N; (i) X56S, X69V, X136W, and X265T; (j) X28P, X69V, and X136W; and (k) X69V, X124I, X136W, and X215F.

In some embodiments, various other combinations of the disclosed amino acid differences can be combined in the engineered polypeptides as disclosed herein and provide various improved enzyme properties. Exemplary engineered polypeptides having various combinations of amino acid differences resulting in improved properties are disclosed in Tables 2A, 2B, 2C, and 2D, and the Examples. The amino acid sequences are provided in the sequence listing incorporated by reference herein and include SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206.

The present disclosure provides polynucleotides encoding the engineered transaminase polypeptides capable of converting a racemic mixture of compound (1) to compound (2a) in at least a 2:1 diastereomeric ratio relative to compound (2c), as well as expression vectors comprising the polynucleotides, and host cells capable of expressing the polynucleotides encoding the polypeptides. Accordingly, in some embodiments, the present disclosure also provides methods of manufacturing the engineered transaminase polypeptides capable of converting compound (1a) to compound (2a), wherein the methods comprise culturing a host cell capable of expressing a polynucleotide encoding the engineered transaminase polypeptide and isolating the polypeptide from the host cell. Exemplary polynucleotide sequences are provided in the sequence listing incorporated by reference herein and include SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, and 205.

In some embodiments, any of the engineered transaminase polypeptides of the present disclosure can be used in improved processes for the preparation of compound (2a) due to their improved enzymatic properties including, production of high enantiomeric excess of R-amine products (e.g., at least about 98% e.e.), high diastereomeric ratio of the trans R-amine product of compound (2a) (e.g., at least about 2:1 d.r.), increased activity (e.g., at least about 2-fold increased activity relative to SEQ ID NO:2), high percent conversion (e.g., at least about 90% conversion in 24 h), in the presence of high substrate loadings (e.g., at least about 40 g/L a racemic mixture of compound (1)), and using isopropylamine as the amino donor. Accordingly, in some embodiments, the present disclosure provides methods using the engineered transaminase polypeptides for preparing compound (2a) in enantiomeric and diastereomeric excess, wherein the methods comprise: contacting compound (1a) with an engineered transaminase polypeptide of the present disclosure (e.g., as described in Table 2 and elsewhere herein) in the presence of an amino donor under suitable reaction conditions. The process can further comprising preparing compound (3) from compound (2a). Suitable reactions conditions for the conversion of compound (1a) to compound (2a), or its salts, hydrates, or solvates, using the engineered transaminase polypeptides of the present disclosure are described in greater detail below, including but not limited to ranges of pH, temperature, buffer, solvent system, substrate loading, mixture of substrate enantiomers (e.g., racemic mixture of compound (1)), polypeptide loading, amino donor loading, atmosphere, and reaction time.

In some embodiments, an analog of compound (2a) can be prepared in enantiomeric and diastereomeric excess from an analog of compound (1a) using engineered transaminase polypeptides in the above described methods. Accordingly, in some embodiments a method for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein the analog of compound (1a) is a compound of Formula I

wherein, Ar is an optionally substituted aromatic ring selected from phenyl, fused phenyl, heteroaryl, or fused heteroaryl; X is selected from N, O, CH₂, and S; m=1 to 6; n=1 to 6; and the analog of compound (2a) prepared is a compound of Formula II

Additionally, the methods using the engineered transaminase polypeptides of the present disclosure to convert compound (1a) to compound (2a) can be used as a step in a process for the preparation of compound (3), or its salts, hydrates, or solvates, wherein, the step in the process comprises contacting compound (1a) with any of the engineered transaminase polypeptides of the present disclosure in the presence of an amino donor under reaction conditions suitable for conversion of compound (1a) to compound (2a) in enantiomeric and diastereomeric excess.

5. DETAILED DESCRIPTION

As used in this specification and the appended claims, the singular forms “a”, “an” and “the” include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to “a polypeptide” includes more than one polypeptide.

Similarly, “comprise,” “comprises,” “comprising” “include,” “includes,” and “including” are interchangeable and not intended to be limiting.

It is to be further understood that where descriptions of various embodiments use the term “comprising,” those skilled in the art would understand that in some specific instances, an embodiment can be alternatively described using language “consisting essentially of” or “consisting of.”

It is to be understood that both the foregoing general description, including the drawings, and the following detailed description are exemplary and explanatory only and are not restrictive of this disclosure.

The section headings used herein are for organizational purposes only and not to be construed as limiting the subject matter described.

5.1 ABBREVIATIONS

The abbreviations used for the genetically encoded amino acids are conventional and are as follows:

Three-Letter One-Letter Amino Acid Abbreviation Abbreviation Alanine Ala A Arginine Arg R Asparagine Asn N Aspartate Asp D Cysteine Cys C Glutamate Glu E Glutamine Gln Q Glycine Gly G Histidine HIS H Isoleucine Ile I Leucine Leu L Lysine Lys K Methionine Met M Phenylalanine Phe F Proline Pro P Serine Ser S Threonine Thr T Tryptophan Trp W Tyrosine Tyr Y Valine Val V

When the three-letter abbreviations are used, unless specifically preceded by an “L” or a “D” or clear from the context in which the abbreviation is used, the amino acid may be in either the L- or D-configuration about α-carbon (C_(α)). For example, whereas “Ala” designates alanine without specifying the configuration about the α-carbon, “D-Ala” and “L-Ala” designate D-alanine and L-alanine, respectively. When the one-letter abbreviations are used, upper case letters designate amino acids in the L-configuration about the α-carbon and lower case letters designate amino acids in the D-configuration about the α-carbon. For example, “A” designates L-alanine and “a” designates D-alanine. When polypeptide sequences are presented as a string of one-letter or three-letter abbreviations (or mixtures thereof), the sequences are presented in the amino (N) to carboxy (C) direction in accordance with common convention.

The abbreviations used for the genetically encoding nucleosides are conventional and are as follows: adenosine (A); guanosine (G); cytidine (C); thymidine (T); and uridine (U). Unless specifically delineated, the abbreviated nucleotides may be either ribonucleosides or 2′-deoxyribonucleosides. The nucleosides may be specified as being either ribonucleosides or 2′-deoxyribonucleosides on an individual basis or on an aggregate basis. When nucleic acid sequences are presented as a string of one-letter abbreviations, the sequences are presented in the 5′ to 3′ direction in accordance with common convention, and the phosphates are not indicated.

5.2 Definitions

In reference to the present disclosure, the technical and scientific terms used in the descriptions herein will have the meanings commonly understood by one of ordinary skill in the art, unless specifically defined otherwise. Accordingly, the following terms are intended to have the following meanings:

“Protein”, “polypeptide,” and “peptide” are used interchangeably herein to denote a polymer of at least two amino acids covalently linked by an amide bond, regardless of length or post-translational modification (e.g., glycosylation, phosphorylation, lipidation, myristilation, ubiquitination, etc.). Included within this definition are D- and L-amino acids, and mixtures of D- and L-amino acids.

“Transaminase” or “aminotransferase” are used interchangeably herein to refer to a polypeptide having an enzymatic capability of transferring an amino group (NH2), a pair of electrons, and a proton from a primary amine to a carbonyl group (C═O) of an acceptor molecule. Transaminases as used herein include naturally occurring (wild type) transaminase as well as non-naturally occurring engineered polypeptides generated by human manipulation.

“Amino acceptor” and “amine acceptor,” “keto substrate,” “keto,” and “ketone” are used interchangeably herein to refer to a carbonyl (keto, or ketone) compound which accepts an amino group from a donor amine Amino acceptors are molecules of general formula shown below,

in which each of R¹, R², when taken independently, is an alkyl, an alkylaryl group, or aryl group which is unsubstituted or substituted with one or more enzymatically acceptable groups. R¹ may be the same or different from R² in structure or chirality. In some embodiments, R¹ and R², taken together, may form a ring that is unsubstituted, substituted, or fused to other rings Amino acceptors include keto carboxylic acids and alkanones (ketones). Typical keto carboxylic acids are α-keto carboxylic acids such as glyoxalic acid, pyruvic acid, oxaloacetic acid, and the like, as well as salts of these acids Amino acceptors also include substances which are converted to an amino acceptor by other enzymes or whole cell processes, such as fumaric acid (which can be converted to oxaloacetic acid), glucose (which can be converted to pyruvate), lactate, maleic acid, and others Amino acceptors that can be used include, by way of example and not limitation, (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone, 3,4-dihydronaphthalen-1(2H)-one, 1-phenylbutan-2-one, 3,3-dimethylbutan-2-one, octan-2-one, ethyl 3-oxobutanoate, 4-phenylbutan-2-one, 1-(4-bromophenyl)ethanone, 2-methyl-cyclohexamone, 7-methoxy-2-tetralone, 1-hydroxybutan-2-one, pyruvic acid, acetophenone, (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone, 2-methoxy-5-fluoroacetophenone, levulinic acid, 1-phenylpropan-1-one, 1-(4-bromophenyl)propan-1-one, 1-(4-nitrophenyl)propan-1-one, 1-phenylpropan-2-one, 2-oxo-3-methylbutanoic acid, 1-(3-trifluoromethylphenyl)propan-1-one, hydroxypropanone, methoxyoxypropanone, 1-phenylbutan-1-one, 1-(2,5-dimethoxy-4-methylphenyl)butan-2-one, 1-(4-hydroxyphenyl)butan-3-one, 2-acetylnaphthalene, phenylpyruvic acid, 2-ketoglutaric acid, and 2-ketosuccinic acid, including both (R) and (S) single isomers where possible.

“Amino donor” or “amine donor” refers to an amino compound which donates an amino group to the amino acceptor, thereby becoming a carbonyl species Amino donors are molecules of general formula shown below,

in which each of R³, R⁴, when taken independently, is an alkyl, an alkylaryl group, or aryl group which is unsubstituted or substituted with one or more enzymatically non-inhibiting groups. R³ can be the same or different from R⁴ in structure or chirality. In some embodiments, R³ and R⁴, taken together, may form a ring that is unsubstituted, substituted, or fused to other rings. Typical amino donors that can be used with the embodiments of the present disclosure include chiral and achiral amino acids, and chiral and achiral amines Amino donors that can be used with the embodiments herein include, by way of example and not limitation, isopropylamine (also referred to as 2-aminopropane, and referred to elsewhere herein as “IPM”), α-phenethylamine (also termed 1-phenylethanamine), and its enantiomers (S)-1-phenylethanamine and (R)-1-phenylethanamine, 2-amino-4-phenylbutane, glycine, L-glutamic acid, L-glutamate, monosodium glutamate, L-alanine, D-alanine, D,L-alanine, L-aspartic acid, L-lysine, D,L-ornithine, β-alanine, taurine, n-octylamine, cyclohexylamine, 1,4-butanediamine (also referred to as putrescine), 1,6-hexanediamine, 6-aminohexanoic acid, 4-aminobutyric acid, tyramine, and benzyl amine, 2-aminobutane, 2-amino-1-butanol, 1-amino-1-phenylethane, 1-amino-1-(2-methoxy-5-fluorophenyl)ethane, 1-amino-1-phenylpropane, 1-amino-1-(4-hydroxyphenyl)propane, 1-amino-1-(4-bromophenyl)propane, 1-amino-1-(4-nitrophenyl)propane, 1-phenyl-2-aminopropane, 1-(3-trifluoromethylphenyl)-2-aminopropane, 2-aminopropanol, 1-amino-1-phenylbutane, 1-phenyl-2-aminobutane, 1-(2,5-dimethoxy-4-methylphenyl)-2-aminobutane, 1-phenyl-3-aminobutane, 1-(4-hydroxyphenyl)-3-aminobutane, 1-amino-2-methylcyclopentane, 1-amino-3-methylcyclopentane, 1-amino-2-methylcyclohexane, 1-amino-1-(2-naphthyl)ethane, 3-methylcyclopentylamine, 2-methylcyclopentylamine, 2-ethylcyclopentylamine, 2-methylcyclohexylamine, 3-methylcyclohexylamine, 1-aminotetralin, 2-aminotetralin, 2-amino-5-methoxytetralin, and 1-aminoindan, including both (R) and (S) single isomers where possible and including all possible salts of the amines.

“Chiral amine” refers to amines of general formula R¹—CH(NH₂)—R² and is employed herein in its broadest sense, including a wide variety of aliphatic and alicyclic compounds of different, and mixed, functional types, characterized by the presence of a primary amino group bound to a secondary carbon atom which, in addition to a hydrogen atom, carries either (i) a divalent group forming a chiral cyclic structure, or (ii) two substituents (other than hydrogen) differing from each other in structure or chirality. Divalent groups forming a chiral cyclic structure include, for example, 2-methylbutane-1,4-diyl, pentane-1,4-diyl, hexane-1,4-diyl, hexane-1,5-diyl, 2-methylpentane-1,5-diyl. The two different substituents on the secondary carbon atom (R¹ and R² above) also can vary widely and include alkyl, aralkyl, aryl, halo, hydroxy, lower alkyl, lower alkoxy, lower alkylthio, cycloalkyl, carboxy, carbalkoxy, carbamoyl, mono- and di-(lower alkyl) substituted carbamoyl, trifluoromethyl, phenyl, nitro, amino, mono- and di-(lower alkyl) substituted amino, alkylsulfonyl, arylsulfonyl, alkylcarboxamido, arylcarboxamido, etc., as well as alkyl, aralkyl, or aryl substituted by the foregoing.

“Pyridoxal-phosphate,” “PLP,” “pyridoxal-5′-phosphate,” “PYP,” and “P5P” are used interchangeably herein to refer to the compound that acts as a cofactor in transaminase reactions. In some embodiments, pyridoxal phosphate is defined by the structure 1-(4′-formyl-3′-hydroxy-2′-methyl-5′-pyridyl)methoxyphosphonic acid, CAS number [54-47-7], Pyridoxal-5′-phosphate can be produced in vivo by phosphorylation and oxidation of pyridoxol (also known as Vitamin B₆). In transamination reactions using transaminase enzymes, the amine group of the amino donor is transferred to the cofactor to produce a keto byproduct, while pyridoxal-5′-phosphate is converted to pyridoxamine phosphate. Pyridoxal-5′-phosphate is regenerated by reaction with a different keto compound (the amino acceptor). The transfer of the amine group from pyridoxamine phosphate to the amino acceptor produces a chiral amine and regenerates the cofactor. In some embodiments, the pyridoxal-5′-phosphate can be replaced by other members of the vitamin B₆ family, including pyridoxine (PN), pyridoxal (PL), pyridoxamine (PM), and their phosphorylated counterparts; pyridoxine phosphate (PNP), and pyridoxamine phosphate (PMP).

“Cofactor,” as used herein, refers to a non-protein compound that operates in combination with an enzyme in catalyzing a reaction. As used herein, “cofactor” is intended to encompass the vitamin B₆ family compounds PLP, PN, PL, PM, PNP, and PMP, which are sometimes also referred to as coenzymes.

“Coding sequence” refers to that portion of a nucleic acid (e.g., a gene) that encodes an amino acid sequence of a protein.

“Naturally-occurring” or “wild-type” refers to the form found in nature. For example, a naturally occurring or wild-type polypeptide or polynucleotide sequence is a sequence present in an organism that can be isolated from a source in nature and which has not been intentionally modified by human manipulation.

“Recombinant” or “engineered” or “non-naturally occurring” when used with reference to, e.g., a cell, nucleic acid, or polypeptide, refers to a material, or a material corresponding to the natural or native form of the material, that has been modified in a manner that would not otherwise exist in nature, or is identical thereto but produced or derived from synthetic materials and/or by manipulation using recombinant techniques. Non-limiting examples include, among others, recombinant cells expressing genes that are not found within the native (non-recombinant) form of the cell or express native genes that are otherwise expressed at a different level.

“Percentage of sequence identity” and “percentage homology” are used interchangeably herein to refer to comparisons among polynucleotides and polypeptides, and are determined by comparing two optimally aligned sequences over a comparison window, wherein the portion of the polynucleotide or polypeptide sequence in the comparison window may comprise additions or deletions (i.e., gaps) as compared to the reference sequence for optimal alignment of the two sequences. The percentage may be calculated by determining the number of positions at which the identical nucleic acid base or amino acid residue occurs in both sequences to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Alternatively, the percentage may be calculated by determining the number of positions at which either the identical nucleic acid base or amino acid residue occurs in both sequences or a nucleic acid base or amino acid residue is aligned with a gap to yield the number of matched positions, dividing the number of matched positions by the total number of positions in the window of comparison and multiplying the result by 100 to yield the percentage of sequence identity. Those of skill in the art appreciate that there are many established algorithms available to align two sequences. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith and Waterman, 1981, Adv. Appl. Math. 2:482, by the homology alignment algorithm of Needleman and Wunsch, 1970, J. Mol. Biol. 48:443, by the search for similarity method of Pearson and Lipman, 1988, Proc. Natl. Acad. Sci. USA 85:2444, by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the GCG Wisconsin Software Package), or by visual inspection (see generally, Current Protocols in Molecular Biology, F. M. Ausubel et al., eds., Current Protocols, a joint venture between Greene Publishing Associates, Inc. and John Wiley & Sons, Inc., (1995 Supplement) (Ausubel)). Examples of algorithms that are suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., 1990, J. Mol. Biol. 215: 403-410 and Altschul et al., 1977, Nucleic Acids Res. 3389-3402, respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information website. This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as, the neighborhood word score threshold (Altschul et al, supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are then extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N (penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) of 10, M=5, N=−4, and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength (W) of 3, an expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff and Henikoff, 1989, Proc Natl Acad Sci USA 89:10915). Exemplary determination of sequence alignment and % sequence identity can employ the BESTFIT or GAP programs in the GCG Wisconsin Software package (Accelrys, Madison Wis.), using default parameters provided.

“Reference sequence” refers to a defined sequence used as a basis for a sequence comparison. A reference sequence may be a subset of a larger sequence, for example, a segment of a full-length gene or polypeptide sequence. Generally, a reference sequence is at least 20 nucleotide or amino acid residues in length, at least 25 residues in length, at least 50 residues in length, or the full length of the nucleic acid or polypeptide. Since two polynucleotides or polypeptides may each (1) comprise a sequence (i.e., a portion of the complete sequence) that is similar between the two sequences, and (2) may further comprise a sequence that is divergent between the two sequences, sequence comparisons between two (or more) polynucleotides or polypeptide are typically performed by comparing sequences of the two polynucleotides or polypeptides over a “comparison window” to identify and compare local regions of sequence similarity. In some embodiments, a “reference sequence” can be based on a primary amino acid sequence, where the reference sequence is a sequence that can have one or more changes in the primary sequence. For instance, a “reference sequence based on SEQ ID NO:2 having at the residue corresponding to X9a threonine” refers to a reference sequence in which the corresponding residue at X9 in SEQ ID NO:2, which is a alanine, has been changed to threonine.

“Comparison window” refers to a conceptual segment of at least about 20 contiguous nucleotide positions or amino acids residues wherein a sequence may be compared to a reference sequence of at least 20 contiguous nucleotides or amino acids and wherein the portion of the sequence in the comparison window may comprise additions or deletions (i.e., gaps) of 20 percent or less as compared to the reference sequence (which does not comprise additions or deletions) for optimal alignment of the two sequences. The comparison window can be longer than 20 contiguous residues, and includes, optionally 30, 40, 50, 100, or longer windows.

“Corresponding to”, “reference to” or “relative to” when used in the context of the numbering of a given amino acid or polynucleotide sequence refers to the numbering of the residues of a specified reference sequence when the given amino acid or polynucleotide sequence is compared to the reference sequence. In other words, the residue number or residue position of a given polymer is designated with respect to the reference sequence rather than by the actual numerical position of the residue within the given amino acid or polynucleotide sequence. For example, a given amino acid sequence, such as that of an engineered transaminase, can be aligned to a reference sequence by introducing gaps to optimize residue matches between the two sequences. In these cases, although the gaps are present, the numbering of the residue in the given amino acid or polynucleotide sequence is made with respect to the reference sequence to which it has been aligned.

“Amino acid difference” or “residue difference” refers to a change in the amino acid residue at a position of a polypeptide sequence relative to the amino acid residue at a corresponding position in a reference sequence. The positions of amino acid differences generally are referred to herein as “Xn,” where n refers to the corresponding position in the reference sequence upon which the residue difference is based. For example, a “residue difference at position X3 as compared to SEQ ID NO: 2” refers to a change of the amino acid residue at the polypeptide position corresponding to position 3 of SEQ ID NO:2. Thus, if the reference polypeptide of SEQ ID NO: 2 has a glutamine at position 3, then a “residue difference at position X3 as compared to SEQ ID NO:2” an amino acid substitution of any residue other than glutamine at the position of the polypeptide corresponding to position 3 of SEQ ID NO: 2. In most instances herein, the specific amino acid residue difference at a position is indicated as “XnY” where “Xn” specified the corresponding position as described above, and “Y” is the single letter identifier of the amino acid found in the engineered polypeptide (i.e., the different residue than in the reference polypeptide). In some instances (e.g., in Tables 2A, 2B, 2C, and 2D), the present disclosure also provides specific amino acid differences denoted by the conventional notation “AnB”, where A is the single letter identifier of the residue in the reference sequence, “n” is the number of the residue position in the reference sequence, and B is the single letter identifier of the residue substitution in the sequence of the engineered polypeptide. In some instances, a polypeptide of the present disclosure can include one or more amino acid residue differences relative to a reference sequence, which is indicated by a list of the specified positions where changes are made relative to the reference sequence. The present disclosure includes engineered polypeptide sequences comprising one or more amino acid differences that include either/or both conservative and non-conservative amino acid substitutions.

“Conservative amino acid substitution” refers to a substitution of a residue with a different residue having a similar side chain, and thus typically involves substitution of the amino acid in the polypeptide with amino acids within the same or similar defined class of amino acids. By way of example and not limitation, an amino acid with an aliphatic side chain may be substituted with another aliphatic amino acid, e.g., alanine, valine, leucine, and isoleucine; an amino acid with hydroxyl side chain is substituted with another amino acid with a hydroxyl side chain, e.g., serine and threonine; an amino acids having aromatic side chains is substituted with another amino acid having an aromatic side chain, e.g., phenylalanine, tyrosine, tryptophan, and histidine; an amino acid with a basic side chain is substituted with another amino acid with a basis side chain, e.g., lysine and arginine; an amino acid with an acidic side chain is substituted with another amino acid with an acidic side chain, e.g., aspartic acid or glutamic acid; and a hydrophobic or hydrophilic amino acid is replaced with another hydrophobic or hydrophilic amino acid, respectively. Exemplary conservative substitutions are provided in Table 1 below:

TABLE 1 Residue Possible Conservative Substitutions A, L, V, I Other aliphatic (A, L, V, I) Other non-polar (A, L, V, I, G, M) G, M Other non-polar (A, L, V, I, G, M) D, E Other acidic (D, E) K, R Other basic (K, R) N, Q, S, T Other polar H, Y, W, F Other aromatic (H, Y, W, F) C, P None

“Non-conservative substitution” refers to substitution of an amino acid in the polypeptide with an amino acid with significantly differing side chain properties. Non-conservative substitutions may use amino acids between, rather than within, the defined groups and affects (a) the structure of the peptide backbone in the area of the substitution (e.g., proline for glycine) (b) the charge or hydrophobicity, or (c) the bulk of the side chain. By way of example and not limitation, an exemplary non-conservative substitution can be an acidic amino acid substituted with a basic or aliphatic amino acid; an aromatic amino acid substituted with a small amino acid; and a hydrophilic amino acid substituted with a hydrophobic amino acid.

“Deletion” refers to modification to the polypeptide by removal of one or more amino acids from the reference polypeptide. Deletions can comprise removal of 1 or more amino acids, 2 or more amino acids, 5 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, up to 10% of the total number of amino acids, or up to 20% of the total number of amino acids making up the reference enzyme while retaining enzymatic activity and/or retaining the improved properties of an engineered transaminase enzyme. Deletions can be directed to the internal portions and/or terminal portions of the polypeptide. In various embodiments, the deletion can comprise a continuous segment or can be discontinuous.

“Insertion” refers to modification to the polypeptide by addition of one or more amino acids from the reference polypeptide. In some embodiments, the improved engineered transaminase enzymes comprise insertions of one or more amino acids to the naturally occurring transaminase polypeptide as well as insertions of one or more amino acids to other improved transaminase polypeptides. Insertions can be in the internal portions of the polypeptide, or to the carboxy or amino terminus. Insertions as used herein include fusion proteins as is known in the art. The insertion can be a contiguous segment of amino acids or separated by one or more of the amino acids in the naturally occurring polypeptide.

“Fragment” as used herein refers to a polypeptide that has an amino-terminal and/or carboxy-terminal deletion, but where the remaining amino acid sequence is identical to the corresponding positions in the sequence. Fragments can be at least 14 amino acids long, at least 20 amino acids long, at least 50 amino acids long or longer, and up to 70%, 80%, 90%, 95%, 98%, and 99% of a full-length transaminase polypeptide.

“Isolated polypeptide” refers to a polypeptide which is substantially separated from other contaminants that naturally accompany it, e.g., protein, lipids, and polynucleotides. The term embraces polypeptides which have been removed or purified from their naturally-occurring environment or expression system (e.g., host cell or in vitro synthesis). The improved transaminase enzymes may be present within a cell, present in the cellular medium, or prepared in various forms, such as lysates or isolated preparations. As such, in some embodiments, the improved transaminase enzyme can be an isolated polypeptide.

“Substantially pure polypeptide” refers to a composition in which the polypeptide species is the predominant species present (i.e., on a molar or weight basis it is more abundant than any other individual macromolecular species in the composition), and is generally a substantially purified composition when the object species comprises at least about 50 percent of the macromolecular species present by mole or % weight. Generally, a substantially pure transaminase composition will comprise about 60% or more, about 70% or more, about 80% or more, about 90% or more, about 95% or more, and about 98% or more of all macromolecular species by mole or % weight present in the composition. In some embodiments, the object species is purified to essential homogeneity (i.e., contaminant species cannot be detected in the composition by conventional detection methods) wherein the composition consists essentially of a single macromolecular species. Solvent species, small molecules (<500 Daltons), and elemental ion species are not considered macromolecular species. In some embodiments, the isolated improved transaminases polypeptide is a substantially pure polypeptide composition.

“Stereoselectivity” refers to the preferential formation in a chemical or enzymatic reaction of one stereoisomer over another. Stereoselectivity can be partial, where the formation of one stereoisomer is favored over the other, or it may be complete where only one stereoisomer is formed. When the stereoisomers are enantiomers, the stereoselectivity is referred to as enantioselectivity, the fraction (typically reported as a percentage) of one enantiomer in the sum of both. It is commonly alternatively reported in the art (typically as a percentage) as the enantiomeric excess (e.e.) calculated therefrom according to the formula [major enantiomer−minor enantiomer]/[major enantiomer+minor enantiomer]. Where the stereoisomers are diastereoisomers, the stereoselectivity is referred to as diastereoselectivity, the fraction (typically reported as a percentage) of one diastereomer in a mixture of two diastereomers, commonly alternatively reported as the diastereomeric excess (d.e.). Where a mixture contains more than two diastereomers it is common to report the ratio of diastereomers or “diastereomeric ratio” rather than diastereomeric excess. Enantiomeric excess and diastereomeric excess are types of stereomeric excess. “Highly stereoselective” refers to a transaminase polypeptide that is capable of converting the substrate to the corresponding chiral amine product with at least about 85% stereomeric excess.

“Improved enzyme property” refers to a transaminase polypeptide that exhibits an improvement in any enzyme property as compared to a reference transaminase. For the engineered transaminase polypeptides described herein, the comparison is generally made to the wild-type transaminase enzyme, although in some embodiments, the reference transaminase can be another improved engineered transaminase. Enzyme properties for which improvement is desirable include, but are not limited to, enzymatic activity (which can be expressed in terms of percent conversion of the substrate), thermo stability, solvent stability, pH activity profile, cofactor requirements, refractoriness to inhibitors (e.g., substrate or product inhibition), stereospecificity, and stereoselectivity (including enantioselectivity).

“Increased enzymatic activity” refers to an improved property of the engineered transaminase polypeptides, which can be represented by an increase in specific activity (e.g., product produced/time/weight protein) or an increase in percent conversion of the substrate to the product (e.g., percent conversion of starting amount of substrate to product in a specified time period using a specified amount of transaminase) as compared to the reference transaminase enzyme. Exemplary methods to determine enzyme activity are provided in the Examples. Any property relating to enzyme activity may be affected, including the classical enzyme properties of K_(m), V_(max) or k_(cat), changes of which can lead to increased enzymatic activity. Improvements in enzyme activity can be from about 1.1 times the enzymatic activity of the corresponding wild-type transaminase enzyme, to as much as 2 times, 5 times, 10 times, 20 times, 25 times, 50 times, 75 times, 100 times, or more enzymatic activity than the naturally occurring transaminase or another engineered transaminase from which the transaminase polypeptides were derived. In specific embodiments, the engineered transaminase enzyme exhibits improved enzymatic activity in the range of 1.5 to 50 times, 1.5 to 100 times greater than that of the parent transaminase enzyme. It is understood by the skilled artisan that the activity of any enzyme is diffusion limited such that the catalytic turnover rate cannot exceed the diffusion rate of the substrate, including any required cofactors. The theoretical maximum of the diffusion limit, or k_(cat)/K_(m), is generally about 10⁸ to 10⁹ (M⁻¹ s⁻¹). Hence, any improvements in the enzyme activity of the transaminase will have an upper limit related to the diffusion rate of the substrates acted on by the transaminase enzyme. Transaminase activity can be measured by any one of standard assays, such as by monitoring changes in spectrophotometric properties of reactants or products. In some embodiments, the amount of products produced can be measured by High-Performance Liquid Chromatography (HPLC) separation combined with UV absorbance or fluorescent detection following o-phthaldialdehyde (OPA) derivatization. Comparisons of enzyme activities are made using a defined preparation of enzyme, a defined assay under a set condition, and one or more defined substrates, as further described in detail herein. Generally, when lysates are compared, the numbers of cells and the amount of protein assayed are determined as well as use of identical expression systems and identical host cells to minimize variations in amount of enzyme produced by the host cells and present in the lysates.

“Conversion” refers to the enzymatic conversion of the substrate(s) to the corresponding product(s). “Percent conversion” refers to the percent of the substrate that is converted to the product within a period of time under specified conditions. Thus, the “enzymatic activity” or “activity” of a transaminase polypeptide can be expressed as “percent conversion” of the substrate to the product.

“Thermostable” refers to a transaminase polypeptide that maintains similar activity (more than 60% to 80% for example) after exposure to elevated temperatures (e.g., 40-80° C.) for a period of time (e.g., 0.5-24 hrs) compared to the wild-type enzyme.

“Solvent stable” refers to a transaminase polypeptide that maintains similar activity (more than e.g., 60% to 80%) after exposure to varying concentrations (e.g., 5-99%) of solvent (ethanol, isopropyl alcohol, dimethylsulfoxide (DMSO), tetrahydrofuran, 2-methyltetrahydrofuran, acetone, toluene, butyl acetate, methyl tert-butyl ether, etc.) for a period of time (e.g., 0.5-24 hrs) compared to the wild-type enzyme.

“Thermo- and solvent stable” refers to a transaminase polypeptide that is both thermostable and solvent stable.

“Derived from” as used herein in the context of engineered transaminase enzymes, identifies the originating transaminase enzyme, and/or the gene encoding such transaminase enzyme, upon which the engineering was based. For example, the engineered transaminase enzyme of SEQ ID NO:34 was obtained by artificially evolving, over multiple generations the gene encoding the Arthrobacter sp. KNK168 transaminase enzyme of SEQ ID NO:2. Thus, this engineered transaminase enzyme is “derived from” the wild-type transaminase of SEQ ID NO:2.

“Stringent hybridization” is used herein to refer to conditions under which nucleic acid hybrids are stable. As known to those of skill in the art, the stability of hybrids is reflected in the melting temperature (T_(m)) of the hybrids. In general, the stability of a hybrid is a function of ion strength, temperature, G/C content, and the presence of chaotropic agents. The T_(m) values for polynucleotides can be calculated using known methods for predicting melting temperatures (see, e.g., Baldino et al., Methods Enzymology 168:761-777; Bolton et al., 1962, Proc. Natl. Acad. Sci. USA 48:1390; Bresslauer et al., 1986, Proc. Natl. Acad. Sci. USA 83:8893-8897; Freier et al., 1986, Proc. Natl. Acad. Sci. USA 83:9373-9377; Kierzek et al., Biochemistry 25:7840-7846; Rychlik et al., 1990, Nucleic Acids Res 18:6409-6412 (erratum, 1991, Nucleic Acids Res 19:698); Sambrook et al., supra); Suggs et al., 1981, In Developmental Biology Using Purified Genes (Brown et al., eds.), pp. 683-693, Academic Press; and Wetmur, 1991, Crit Rev Biochem Mol Biol 26:227-259. All publications incorporate herein by reference). In some embodiments, the polynucleotide encodes the polypeptide disclosed herein and hybridizes under defined conditions, such as moderately stringent or highly stringent conditions, to the complement of a sequence encoding an engineered transaminase enzyme of the present disclosure.

“Hybridization stringency” relates to hybridization conditions, such as washing conditions, in the hybridization of nucleic acids. Generally, hybridization reactions are performed under conditions of lower stringency, followed by washes of varying but higher stringency. The term “moderately stringent hybridization” refers to conditions that permit target-DNA to bind a complementary nucleic acid that has about 60% identity, preferably about 75% identity, about 85% identity to the target DNA, with greater than about 90% identity to target-polynucleotide. Exemplary moderately stringent conditions are conditions equivalent to hybridization in 50% formamide, 5× Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.2×SSPE, 0.2% SDS, at 42° C. “High stringency hybridization” refers generally to conditions that are about 10° C. or less from the thermal melting temperature T_(m) as determined under the solution condition for a defined polynucleotide sequence. In some embodiments, a high stringency condition refers to conditions that permit hybridization of only those nucleic acid sequences that form stable hybrids in 0.018M NaCl at 65° C. (i.e., if a hybrid is not stable in 0.018M NaCl at 65° C., it will not be stable under high stringency conditions, as contemplated herein). High stringency conditions can be provided, for example, by hybridization in conditions equivalent to 50% formamide, 5× Denhart's solution, 5×SSPE, 0.2% SDS at 42° C., followed by washing in 0.1×SSPE, and 0.1% SDS at 65° C. Another high stringency condition is hybridizing in conditions equivalent to hybridizing in 5×SSC containing 0.1% (w:v) SDS at 65° C. and washing in 0.1×SSC containing 0.1% SDS at 65° C. Other high stringency hybridization conditions, as well as moderately stringent conditions, are described in the references cited above.

“Codon optimized” refers to changes in the codons of the polynucleotide encoding a protein to those preferentially used in a particular organism such that the encoded protein is efficiently expressed in the organism of interest. Although the genetic code is degenerate in that most amino acids are represented by several codons, called “synonyms” or “synonymous” codons, it is well known that codon usage by particular organisms is nonrandom and biased towards particular codon triplets. This codon usage bias may be higher in reference to a given gene, genes of common function or ancestral origin, highly expressed proteins versus low copy number proteins, and the aggregate protein coding regions of an organism's genome. In some embodiments, the polynucleotides encoding the transaminases enzymes may be codon optimized for optimal production from the host organism selected for expression.

“Preferred, optimal, high codon usage bias codons” refers interchangeably to codons that are used at higher frequency in the protein coding regions than other codons that code for the same amino acid. The preferred codons may be determined in relation to codon usage in a single gene, a set of genes of common function or origin, highly expressed genes, the codon frequency in the aggregate protein coding regions of the whole organism, codon frequency in the aggregate protein coding regions of related organisms, or combinations thereof. Codons whose frequency increases with the level of gene expression are typically optimal codons for expression. A variety of methods are known for determining the codon frequency (e.g., codon usage, relative synonymous codon usage) and codon preference in specific organisms, including multivariate analysis, for example, using cluster analysis or correspondence analysis, and the effective number of codons used in a gene (see GCG CodonPreference, Genetics Computer Group Wisconsin Package; CodonW, John Peden, University of Nottingham; McInerney, J. O, 1998, Bioinformatics 14:372-73; Stenico et al., 1994, Nucleic Acids Res. 222437-46; Wright, F., 1990, Gene 87:23-29). Codon usage tables are available for a growing list of organisms (see for example, Wada et al., 1992, Nucleic Acids Res. 20:2111-2118; Nakamura et al., 2000, Nucl. Acids Res. 28:292; Duret, et al., supra; Henaut and Danchin, “Escherichia coli and Salmonella,” 1996, Neidhardt, et al. Eds., ASM Press, Washington D.C., p. 2047-2066. The data source for obtaining codon usage may rely on any available nucleotide sequence capable of coding for a protein. These data sets include nucleic acid sequences actually known to encode expressed proteins (e.g., complete protein coding sequences-CDS), expressed sequence tags (ESTS), or predicted coding regions of genomic sequences (see for example, Mount, D., Bioinformatics: Sequence and Genome Analysis, Chapter 8, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y., 2001; Uberbacher, E. C., 1996, Methods Enzymol. 266:259-281; Tiwari et al., 1997, Comput. Appl. Biosci. 13:263-270).

“Control sequence” is defined herein to include all components, which are necessary or advantageous for the expression of a polynucleotide and/or polypeptide of the present disclosure. Each control sequence may be native or foreign to the nucleic acid sequence encoding the polypeptide. Such control sequences include, but are not limited to, a leader, polyadenylation sequence, propeptide sequence, promoter, signal peptide sequence, and transcription terminator. At a minimum, the control sequences include a promoter, and transcriptional and translational stop signals. The control sequences may be provided with linkers for the purpose of introducing specific restriction sites facilitating ligation of the control sequences with the coding region of the nucleic acid sequence encoding a polypeptide.

“Operably linked” is defined herein as a configuration in which a control sequence is appropriately placed (i.e., in a functional relationship) at a position relative to a polynucleotide of interest such that the control sequence directs or regulates the expression of the polynucleotide and/or polypeptide of interest.

“Promoter sequence” refers to a nucleic acid sequence that is recognized by a host cell for expression of a polynucleotide of interest, such as a coding sequence. The promoter sequence contains transcriptional control sequences, which mediate the expression of a polynucleotide of interest. The promoter may be any nucleic acid sequence which shows transcriptional activity in the host cell of choice including mutant, truncated, and hybrid promoters, and may be obtained from genes encoding extracellular or intracellular polypeptides either homologous or heterologous to the host cell.

5.3 Engineered Transaminase Polypeptides for the Synthesis of (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine

The present disclosure provides engineered polypeptides having transaminase activity useful for the synthesis of compound (2a), (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine, polynucleotides encoding the engineered polypeptides, and methods for using the engineered polypeptides. Where the description relates to polypeptides, it is to be understood that it also describes the polynucleotides encoding the polypeptides.

Accordingly, in one aspect, the present disclosure relates to engineered transaminase polypeptides which exhibit high stereoselectivity for the R-amine products of compound (2a) and compound (2c) relative to the corresponding S-amine products of compound (2d) and compound (2b), respectively (see Scheme 2 above), and capable of converting a racemic mixture of compound (1) to the R-amine products in an enantiomeric excess of at least 85% e.e., 90% e.e., 95% e.e., 98% e.e., 99% e.e., or more. Additionally, the engineered transaminase polypeptides exhibit diastereoselectivity for the trans R-amine product and are capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions (see Scheme 3 above). These engineered polypeptides are non-naturally occurring transaminases engineered to have improved properties, such as increased stereoselectivity, as compared to the wild-type Arthrobacter sp. KNK168 polypeptide of SEQ ID NO:2, or the engineered polypeptide of SEQ ID NO:4, which has a single amino acid difference (I306V) relative to the wild-type. These engineered transaminase polypeptides are adapted for efficient conversion of (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone to the product (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine and have one or more residue differences as compared to the reference engineered transaminase polypeptide of SEQ ID NO: 6 (which has 24 amino acid differences relative to the wild-type). These residue differences are associated with improvements in enzyme properties, particularly increased stereoselectivity, increased activity, increased thermostability, and tolerance of increased substrate and/or product concentration (e.g., decreased product inhibition).

The engineered polypeptides of the present disclosure have both high enantioselectivity for R-amine products and high diastereoselectivity for the trans relative to the cis amine products. In some embodiments, the engineered polypeptides are capable of converting a racemic mixture of compound (1) to the R-amine products of compound (2a) and compound (2c) in at least 98% e.e. relative to the corresponding S-amine products of compound (2d) and (2b), respectively, and producing the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions. In some embodiments, the engineered transaminase polypeptides are capable of converting the racemic mixture of compound (1) to the R-amine products of compound (2a) and (2c) in an enantiomeric excess relative to the S-amine products of compound (2d) and (2b) of at least about 95% e.e., at least about 96% e.e., at least about 97% e.e., at least about 98% e.e., at least about 99% e.e., or at least about 99.9% e.e. In some embodiments, the engineered transaminase polypeptides are capable of converting the racemic mixture of compound (1) to compound (2a) in even higher diastereomeric ratio relative to compound (2c) of at least about 3:1, at least about 4:1, at least about 8:1, at least about 10:1, at least about 15:1, at least about 20:1, or at least about 30:1, under suitable reaction conditions.

In some embodiments, the engineered polypeptides of the present disclosure are capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) also exhibit increased activity relative to the reference polypeptide of SEQ ID NO: 6. In some embodiments, the engineered transaminase polypeptides are capable of converting the substrate of compound (1a) to compound (2a) with an activity that is increased at least about 1.2 fold, 1.5 fold, 2 fold, 3 fold, 4 fold, 5 fold, 10 fold, 20 fold, 30 fold, 40 fold, 50 fold, 100 fold, relative to the activity of the reference polypeptide of SEQ ID NO: 6, under suitable reaction conditions. In some embodiments, the engineered transaminase polypeptides are capable of converting the substrate of compound (1a) to compound (2a) with a percent conversion of at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%, at least about 95%, at least about 98%, at least about 99%, in a reaction time of about 48 h, about 36 h, about 24 h, or even shorter length of time, under suitable reaction conditions.

In some embodiments, the engineered polypeptides of the present disclosure are capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) also exhibit increased tolerance for the presence of substrate relative to the reference polypeptide of SEQ ID NO: 6 under suitable reaction conditions. Accordingly, in some embodiments the engineered transaminase polypeptides are capable of converting the substrate of compound (1a) to compound (2a) in the presence of a substrate concentration of at least about 20 g/L, about 30 g/L, about 40 g/L, about 50 g/L, about 70 g/L, about 100 g/L, with a percent conversion of at least about 40%, at least about 50%, at least about 60%, at least about 70%, at least about 80%, or at least about 90%, at least about 95%, at least about 98%, at least about 99%, in a reaction time of about 48 h, about 36 h, about 24 h, or even shorter length of time, under suitable reaction conditions.

The suitable reaction conditions under which the above-described improved properties of the engineered polypeptides can be determined can comprise concentrations or amounts of polypeptide, substrate, amine donor, cofactor, buffer, co-solvent, pH, and/or conditions including temperature and reaction time. In some embodiments, the suitable reaction conditions comprise 200 μL total volume, 5 g/L of the racemic mixture of compound (1), 100 μL cell lysate comprising the polypeptide, 1 M isopropylamine (IPM), 1 mM PLP, 100 mM TEA, pH 10.0, 45° C. and 2 h reaction time. In some embodiments, the suitable reaction conditions comprise 10 g/L substrate of the racemic mixture of compound (1), 1 g/L SFP powder of the polypeptide, 1.5 M isopropylamine, 1 g/L PLP, 0.2 M borate buffer, 20% (v/v) DMSO, pH 10.5, 45° C. and 20-24 h reaction time.

Structure and function information for exemplary non-naturally occurring (or engineered) transaminase polypeptides of the present disclosure are shown below in Tables 2A, 2B, 2C, and 2D. The odd numbered sequence identifiers (i.e., SEQ ID NO) refer to the nucleotide sequence encoding the amino acid sequence provided by the even numbered SEQ ID NOs, and the sequences are provided in the electronic sequence listing file accompanying this disclosure, which is hereby incorporated by reference herein. The amino acid residue differences are based on comparison to the reference polypeptide sequence of SEQ ID NO: 6, which is an engineered transaminase polypeptide having the following 24 amino acid differences relative to the naturally occurring transaminase of Arthrobacter sp. KNK168 (SEQ ID NO: 2): S8P; Y60F; L61Y; H62T; V65A; V69T; D81G; M94I; 196L; F1221; G136F; A169L; V1991; A209L; G215C; G217N; S223P; L269P; L273Y; T282S; A284G; P297S; I306V; and S321P. The “trans:cis diastereomeric ratio” (also referred to herein as “d.r.”) refers to the ratio of the two possible trans diastereomer products (e.g., compound (2a) and compound (2d)) to the two possible cis diastereomer products (e.g., compound (2b) and compound (2c)). The trans:cis ratio can be calculated from the formula, [(2a)+(2d)]/[(2b)+(2c)]. However, the engineered transaminase polypeptides of the present disclosure are highly stereoselective for the R-amine products of compound (2a) and compound (2c) and produce little or none of the S-amine compounds of (2b) or (2d). Chiral HPLC analysis of selected engineered polypeptides of the present disclosure showed that the R-amine products produced in at least 98% e.e, which is to be expected because the original wild-type transaminase from which they are derived is R-selective. Consequently, the trans:cis diastereomeric ratio measured herein closely approximates the diastereomeric ratio of compound (2a) to compound (2c). Values for diastereomeric excess (“d.e.”) could also be calculated using the trans to cis ratio based on the assumption of high enantioselectivity for R-amine (e.e. of >98%) as follows: {([(2a)]+[(2d)])−([(2b)]+[(2c)])}/{[(2a)]+[(2b)]+[(2c)]+[(2d)]}.

Initial screening assays of transaminases showed that the engineered polypeptide of SEQ ID NO: 6 converted the substrate racemic mixture of compound (1) to the trans R-amine product of compound (2a) in nearly a 1:1 ratio (0.9 d.r., −5.2% d.e.) with the cis R-amine product of compound (2c). The wild-type transaminase polypeptide of SEQ ID NO: 2 and engineered transaminase of SEQ ID NO: 4, were found to convert the substrate racemic mixture of compound (1) to the undesired cis isomer, (1R,2S)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound (2c)) in a significantly greater ratio than the desired trans R-amine product of compound (2a) (0.08 d.r., −86% d.e.). Consequently, the engineered polypeptide of SEQ ID NO: 6 was used as the starting point for the further evolution of engineered polypeptides capable of providing the trans R-amine product of compound (2a) in at least a 2:1 ratio to the cis R-amine product of compound (2c) described herein.

The stereoselectivity (trans:cis d.r. and/or % d.e.), relative activity, and/or percent conversion, of each engineered polypeptide was determined relative to the positive control reference polypeptide of SEQ ID NO: 6 by measuring conversion of a racemic substrate mixture of compound (1) (i.e., a racemate of the (R)- and (S)-enantiomers of 2-(3,4-dimethoxyphenethoxy)cyclohexanone) to the trans R-amine and cis R-amine products of compound (2a) and compound (2c), respectively using a high-throughput (HTP) assay (as primary screen), and, in some cases, a secondary shake-flask powder (SFP) assay. The HTP assay values in Tables 2A, 2B, 2C, and 2D were determined using E. coli clear cell lysates in 96 well-plate format of ˜200 μL volume per well following assay reaction conditions as noted in the Tables. Further details of and modifications to the HTP assay made for improved screening of engineered polypeptides are noted in Tables 2A, 2B, 2C, and 2D and described in Example 1. The SFP preparations are approximately 30% total protein and provide a more purified preparation of the engineered polypeptide. The SFP assay values in Table 2B were determined using SFP preparations of the engineered polypeptides in a 2.0 mL vial format following assays reaction conditions noted in Table 2B. Further details of and modifications to the SFP assay made for improved screening of engineered polypeptides are described in Example 1.

TABLE 2A Activity² relative to Trans:Cis SEQ ID SEQ Ratio² % d.e.² NO: 6 % Conversion⁵ ID NO: Amino Acid Differences (HTP (HTP (HTP (SFP (nt/aa) (relative to SEQ ID NO: 6) assay¹) assay¹) assay¹) assay^(3,4)) 5/6 N/A 0.9 −5.2 1.00 99⁴ 7/8 S124V; F136W; P210S; 30.9 93.7 0.18 73³  9/10 T69V; F136W; S257F; 25.3 92.4 0.47 11/12 L28P; T69V; F136W; 22.9 91.6 0.59 92³ 13/14 F56S; T69V; F136W; A265T; 19.7 90.4 0.21 15/16 T69V; F136W; 19.4 89.5 0.55 91³ 17/18 T69V; S124I; F136W; 17.0 88.1 0.60 89³ 19/20 A38G; T69V; F136W; 16.1 88.3 0.58 21/22 I10V; H14R; T69V; F136W; 13.8 86.5 0.53 23/24 S124I; F136W; S181G; 13.0 85.7 0.63 25/26 T69V; F136W; A265T; 10.8 83.1 0.41 27/28 S124I; F136W; 10.4 82.5 0.47 29/30 T69V; P99L; F136W; K142R; 9.9 81.6 0.52 31/32 T69V; S124I; 9.3 80.5 0.40 33/34 S124V; F136W; 9.2 80.4 0.57 35/36 T69V; F136W; P210S; 8.7 79.5 0.35 37/38 F136W; L209E; P210S; 8.1 78.0 0.64 39/40 S124V; P210S; 4.0 60.2 0.45 75³ 41/42 T69V; 3.9 58.7 0.49 43/44 T69V; C215Y; 3.7 57.7 0.51 45/46 L209E; 3.6 56.3 0.51 83⁴ 47/48 T69V; N217S; 3.6 56.6 0.50 49/50 A44V; P223N; 3.6 56.0 0.18 51/52 P223N; 3.5 55.0 0.23 39⁴ 53/54 P223L; 3.3 53.8 0.17 55/56 F56L; S124I; 3.1 51.5 0.70 57/58 P223I; 3.1 50.9 0.33 42⁴ 59/60 T7A; S124L; 3.0 49.9 0.72 61/62 I199Y; 2.6 44.9 0.28 63/64 T69W; 2.5 42.1 0.26 65/66 F136W; V171A; 2.4 41.3 1.24 99⁴ 67/68 S124F; G245S; 2.4 40.9 0.47 69/70 L209D; 2.3 40.2 0.33 71/72 S124F; L213P; 2.3 40.1 0.37 73/74 P135Q; 2.3 39.3 0.38 75/76 T69C; 2.2 38.2 0.57 77/78 L209C; A242T; 2.2 37.5 0.08 79/80 S124L; 2.2 37.4 0.81 81/82 F136W; 2.1 36.3 1.25 99⁴ 83/84 S124V; 2.1 35.4 0.75 85/86 I199F; 2.1 35.1 0.64 87/88 I199R; 2.0 33.9 0.65 89/90 P223M; 2.0 32.9 0.27 ¹HTP assay conditions: a total HTP assay volume of 200 μL, 5 g/L of a racemic substrate mixture of compound (1), 100 μL clear cell lysate containing the engineered transaminase polypeptide, 1M isopropylamine (IPM), 1 mM PLP, 100 mM TEA, pH 10.0, 45° C. and 2 h reaction time with 245 rpm shaking. Cells were lysed by shaking for 0.5 to 1 hour at 250 rpm and 37° C. in 1 mL of lysis buffer containing 100 mM triethanolamine, 0.5 g/L lysozyme, and 0.4 g/L polymyxin B sulfate at pH 9.0. ²Stereoselectivity and Activity analysis: “Trans-Cis Ratio,” “% d.e.” and “Activity” were measured using achiral HPLC on either a Luna C18 or Ascentis C18 column as detailed in Example 1. Activity relative to positive control (i.e., SEQ ID NO: 6) was determined as the ratio of percent conversion to the R-amine products (i.e., compound (2a) and (2c)) measured for the engineered polypeptide relative to the positive control polypeptide on the same HTP assay plate after 2 h reaction. Production of the R-amine products relative to S-amine products of 99% e.e. was confirmed using chiral HPLC analysis of polypeptide SFP samples from at least the following: SEQ ID NO: 6, 8, 12, 16, 18, 40, 42, 44, 46, 48, 50, 52, 58, 66, and 82. ³SFP assay conditions: 10 g/L substrate mixture of compound (1), 1.0 g/L of the engineered transaminase polypeptide SFP, 1.0 g/L PLP, 1M IPM, in an aqueous co-solvent solution of 0.2M borate buffer, 20% (v/v) DMSO, pH 10.5, 45° C. reaction temperature and overnight (15-18 h) reaction time. ⁴SFP assay conditions: 10 g/L substrate mixture of compound (1), 1.0 g/L of the engineered transaminase polypeptide SFP, 1.0 g/L PLP, 1M IPM, in an aqueous co-solvent solution of 0.1M triethanolamine buffer, 20% (v/v) DMSO, pH 10.0, 45° C. reaction temperature and 4.5 h reaction time. ⁵% Conversion analysis: Percent conversion was determined using achiral HPLC on an Ascentis C18 column as detailed in Example 1 by measuring the percent of the R-amine products (i.e., compound (2a) and (2c)) produced relative to the amount of racemic mixture of compound (1) for after the stated reaction time for the SFP assay.

TABLE 2B Activity⁴ relative to Trans:Cis SEQ ID SEQ ID Ratio³ NO: 18 NO: Amino Acid Differences (SFP (HTP (nt/aa) (relative to SEQ ID NO: 6) Assay¹) Assay²) SFP Batch 1 17/18 T69V; S124I; F136W; 12.7 1.00 91/92 T69V; S124I; F136W; C215F 18.9 1.73 93/94 T69V; S124I; F136W; W156S; I267V; 27.5 1.49 SFP Batch 2 17/18 T69V; S124I; F136W; 8 1.00 95/96 T69V; S124I; S126T; F136W; Y150N; 10.1 1.29 97/98 T69V; S124I; F136W; Y150A; 10.1 1.50  99/100 T69V; S124I; S126T; F136W; 7.5 1.19 101/102 T69V; S124I; S126A; F136W; 10.9 1.30 ¹SFP assay conditions: 100 g/L substrate mixture of compound (1), 1.0 g/L of the engineered transaminase polypeptide SFP, 1.0 g/L PLP, 1M IPM, in an aqueous co-solvent solution of 0.2M borate buffer, 40% (v/v) DMSO, pH 10.5, 45° C. reaction temperature and 24 h reaction time (with 400 rpm shaking). ²HTP assay conditions: 200 μL total volume, 50 g/L substrate mixture of compound (1), 40 μL of clear cell lysate containing the engineered transaminase polypeptide, 1 g/L PLP, 1M IPM, in an aqueous co-solvent solution of 0.2M borate buffer, 40% (v/v) DMSO, pH 10.5, 45° C. reaction temperature and 4 h reaction time (with 200 rpm shaking). ³Stereoselectivity analysis: “Trans-Cis Ratio” was measured using achiral HPLC on either a Zorbax column after running according to SFP assay conditions, further detailed in Example 1. ⁴Activity analysis: Activity relative to positive control (i.e., SEQ ID NO: 6) was determined as the ratio of percent conversion to the R-amine products (i.e., compound (2a) and (2c)) measured for the engineered polypeptide relative to the positive control polypeptide on the same HTP assay plate after running according to HTP assay conditions, further detailed in Example 1.

TABLE 2C Fold-Improved Fold-Improved SEQ ID Activity^(1,2) Stability^(3,4) NO: Amino Acid Differences (relative to SEQ (relative to SEQ (nt/aa) (relative to SEQ ID NO: 6) ID NO: 92) ID NO: 92) 103/104 I41F; T69V; S124I; F136W; C215F; 1.68 — 105/106 S4L; T69V; S124I; F136W; D165N; C215F; 2.23 — 107/108 S124I; F136W; C215F; 2.19 — 109/110 T69V; S124I; F136W; T141L; C215F; 1.66 — 111/112 T69V; S124I; F136W; K142T; C215F; 1.89 — 113/114 F56G; T69V; S124I; F136W; C215F; 2.02 — 115/116 I55L; T69V; S124I; F136W; C215F; 1.21 — 117/118 T69V; I94L; S124I; F136W; C215F; 1.23 — 119/120 T69V; S124I; F136W; S182T; C215F; 1.20 — 121/122 Q58L; T69V; S124I; F136W; C215F; 1.82 — 123/124 S54P; T69V; S124I; F136W; C215F; 1.48 — 125/126 S54R; T69V; S124I; F136W; C215F; 1.95 — 127/128 S54N; T69V; S124I; F136W; C215F; 1.41 — 129/130 S54K; T69V; S124I; F136W; C215F; 1.84 — 131/132 T69V; S124I; F136W; C215F; I267V; 1.85 — 133/134 T69V; S124I; F136W; W156S; C215F; L218M; 1.53 — 135/136 A5N; A44Q; T69V; I108V; S124I; S126A; 2.12 — F136W; Y150A; C215F; L218M; V328I; 137/138 T69V; S124I; F136W; W156F; C215F; 1.11 — 139/140 T69V; S124I; F136W; W156T; C215F; 1.19 — 141/142 A2K; T69V; S124I; F136W; C215F; 1.91 — 143/144 A2Q; T69V; S124I; F136W; C215F; 1.93 — 145/146 A2S; T69V; S124I; F136W; C215F; 2.13 — 147/148 A2Q; T69V; S124I; F136W; C215F; 1.81 — 149/150 A5S; T69V; S124I; F136W; C215F; 2.86 — 151/152 A5T; T69V; S124I; F136W; C215F; 3.42 — 153/154 A5I; T69V; S124I; F136W; C215F; 3.13 — 155/156 A5H; T69V; S124I; F136W; C215F; 3.20 — 157/158 A5L; T69V; S124I; F136W; C215F; 1.93 — 159/160 A5V; T69V; S124I; F136W; C215F; 2.52 — 161/162 A5L; T69V; S124I; F136W; C215F; 3.52 — 163/164 E9Q; T69V; S124I; F136W; C215F; N296S; 1.70 — 165/166 S4I; T69V; S124I; F136W; C215F; 2.33 — 167/168 E9S; T69V; S124I; F136W; C215F; 1.57 — 169/170 P8T; T69V; S124I; F136W; C215F; 2.02 — 171/172 E9N; T69V; S124I; F136W; C215F; 1.82 — 173/174 S4L; T69V; S124I; F136W; C215F; 1.76 — 175/176 V11K; T69V; S124I; F136W; C215F; 1.88 — 177/178 A2S; A5H; T69V; S124I; S126A; F136W; individual — W156S; C215F; I267V; construct 179/180 A2S; A5H; T69V; S124I; F136W; C215F; individual — construct 181/182 A2S; A5N; A44Q; T69V; I108V; S124I; S126A; individual — F136W; Y150A; C215F; L218M; V328I; construct 183/184 G37R; T69V; S124I; F136W; C215F; — 2.26 185/186 T22I; T69V; S124I; F136W; C215F; — 1.93 187/188 E42A; T69V; S124I; F136W; C215F; — 3.04 189/190 R52K; T69V; S124I; F136W; C215F; — 1.67 191/192 T69V; S124I; F136W; R164A; C215F; — 1.75 193/194 T69V; S124I; F136W; Q155A; C215F; — 2.00 195/196 T69V; S124I; F136W; Y150F; C215F; — 1.71 197/198 T69V; S124I; F136W; W156G; C215F; — 2.68 199/200 T69V; S124I; F136W; W156A; C215F; — 1.78 201/202 T69V; S124I; F136W; W156S; C215F; — 2.20 203/204 T69V; S124I; F136W; I157L; C215F; — 1.83 205/206 A5H; F56G; T69V; I94L; S124I; F136W; C215F; 1.11 — ¹Activity HTP Assay Conditions: a total HTP assay volume of 200 μL, 50 g/L of a racemic substrate mixture of compound (1), 20 μL clear cell lysate containing the engineered transaminase polypeptide, 1M isopropylamine (IPM), 1 g/L PLP, 40% DMSO, 0.2M borate buffer, pH 10.5, 45° C. and 4 h reaction time with 250 rpm shaking. Cells were lysed by shaking for 1 hour at 800 rpm and room temperature in 300 μL of lysis buffer containing 0.2M borate buffer, 0.5 g/L lysozyme, and 0.4 g/L polymyxin B sulfate at pH 10.5. ²Activity Analysis: “Activity” was measured using achiral HPLC on a Ascentis C18 column as detailed in Example 1. Activity relative to positive control (i.e., SEQ ID NO: 92) was determined as the ratio of percent conversion to the R-amine products (i.e., compound (2a) and (2c)) measured for the engineered polypeptide relative to the positive control polypeptide on the same HTP assay plate after 4 h reaction. ³Stability HTP assay conditions: a total HTP assay volume of 200 μL, 40 μL clear cell lysate containing the engineered transaminase polypeptide were incubated in 1M isopropylamine (IPM), 1 g/L PLP, 40% DMSO, 0.2M borate buffer, pH 10.5, 45° C. for 24 h. After incubation the reaction was started with the addition of a racemic substrate mixture of compound (1) to a reaction concentration of 50 g/L. The reaction was let to proceed for 4 h at 45° C. with 250 rpm shaking. Cells were lysed by shaking for 1 hour at 800 rpm and room temperature in 300 μL of lysis buffer containing 0.2M borate buffer, 0.5 g/L lysozyme, and 0.4 g/L polymyxin B sulfate at pH 10.5. ⁴Stability analysis: “Stability” was measured using achiral HPLC on a Ascentis C18 column as detailed in Example 1. Stability relative to positive control (i.e., SEQ ID NO: 92) was determined as the ratio of percent conversion to the R-amine products (i.e., compound (2a) and (2c)) measured for the engineered polypeptide relative to the positive control polypeptide on the same HTP assay plate after 24 h incubation followed by 4 h reaction.

TABLE 2D Activity^(3,4) (relative SEQ ID to SEQ NO: Amino Acid Differences Trans:Cis ID NO: (nt/aa) (relative to SEQ ID NO: 6) Ratio^(1,2) 18) 17/18 T69V; S124I; F136W; 38 1.00 125/126 S54R; T69V; S124I; F136W; C215F; 34 4.34 131/132 T69V; S124I; F136W; C215F; I267V; 19 3.63 155/156 A5H; T69V; S124I; F136W; C215F; 18 4.41 179/180 A2S; A5H; T69V; S124I; F136W; 19 4.98 C215F; 205/206 A5H; F56G; T69V; I94L; S124I; 37 4.37 F136W; C215F; 135/136 A5N; A44Q; T69V; I108V; S124I; 44 2.07 S126A; F136W; Y150A; C215F; L218M; V328I; ¹DSP specificity assay conditions: 100 g/L substrate mixture of compound (1), 5.0 g/L of a DSP powder of the engineered transaminase polypeptide, 1.0 g/L PLP, 1M IPM, in an aqueous co-solvent solution of 0.2M borate buffer, 40% (v/v) DMSO, pH 10.5, 45° C. reaction temperature and 24 h reaction time (with 400 rpm stirring). ²Stereoselectivity analysis: “Trans-Cis Ratio” was measured using achiral HPLC after running according to DSP specificity assay conditions. ³DSP activity assay conditions: 100 g/L substrate mixture of compound (1), 0.5 g/L of a DSP powder of the engineered transaminase polypeptide, 1.0 g/L PLP, 1M IPM, in an aqueous co-solvent solution of 0.2M borate buffer, 40% (v/v) DMSO, pH 10.5, 45° C. reaction temperature and 24 h reaction time (with 400 rpm stirring). ⁴Activity analysis: Activity relative to positive control (i.e., SEQ ID NO: 18) was determined as the ratio of percent conversion to the R-amine products (i.e., compound (2a) and (2c)) measured for the engineered polypeptide relative to the positive control polypeptide on the same DSP assay conditions.

In some embodiments, the engineered transaminase polypeptides of the present disclosure which are capable of converting compound (1a) to compound (2a) comprise an amino acid sequence selected from any one of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206. As shown above in Tables 2A, 2B, 2C, and 2D, each of these exemplary engineered polypeptides comprises one or more amino acid residue differences as compared to SEQ ID NO: 6, and capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions. In some embodiments, the engineered transaminase polypeptides are capable of converting the racemic mixture of compound (1) to compound (2a) in even higher diastereomeric ratio relative to compound (2c) of at least about 3:1, at least about 4:1, at least about 8:1, at least about 10:1, at least about 15:1, at least about 20:1, or at least about 30:1, under suitable reaction conditions. In contrast, engineered transaminase reference polypeptide of SEQ ID NO: 6 is capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in only about 0.9:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c). Additionally, the exemplary engineered transaminase polypeptides of the present disclosure are highly enantioselective for producing R-amine products and capable of converting a racemic mixture of compound (1) to the R-amine products of compound (2a) and compound (2c) in at least 98% e.e. relative to the corresponding S-amine products of compound (2d) and (2b) (as confirmed for the engineered polypeptides of SEQ ID NO: 6, 8, 12, 16, 18, 40, 42, 44, 46, 48, 50, 52, 58, 66, and 82). Due to this combination of high enantioselectivity and high diastereoselectivity, the exemplary engineered transaminase polypeptides are capable of converting racemic mixture of compound (1) to the specific product compound (2a) in higher percentage relative to the other three possible product compounds compared to the wild-type transaminase of SEQ ID NO: 2 or the engineered transaminases of SEQ ID NO: 4 or 6.

The amino acid differences of the exemplary engineered polypeptides associated with their improved properties are shown in Tables 2A, 2B, 2C, and 2D and include one or more residue differences as compared to SEQ ID NO:6 at the following residue positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. The specific amino acid differences as compared to SEQ ID NO:6 at each of these positions that are associated with the improved properties of the exemplary polypeptides of Tables 2A, 2B, 2C, and 2D include: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X69C; X69V; X69W; X94L; X99L; X108V; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X135Q; X136W; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I.

Additionally, certain combinations of amino acid differences of the exemplary engineered polypeptides of Tables 2A, 2B, 2C, and 2D and are associated with their improved properties including the combinations of amino acid differences as compared to SEQ ID NO: 6 selected from: (a) X124V, and X210S; (b) X124V, X136W, and X210S; (c) X69V, and X136W; (d) X69V, and X215Y; (e) X69V, and X217S; (f) X69V, X124I, and X136W; (g) X69V; X136W, and X257F; (h) X44V, and X223N; (i) X56S, X69V, X136W, and X265T; (j) X28P, X69V, and X136W; and (k) X69V, X124I, X136W, and X215F.

In addition to the exemplary engineered polypeptides of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, the present disclosure provides engineered transaminase polypeptides having their improved enzymatic properties (e.g., as disclosed above) and comprising further modifications of the amino acid sequence. Such engineered polypeptides can be derived from the exemplary polypeptides and have amino acid sequences retaining some percent identity to the exemplary engineered polypeptides and one or more of the amino acid differences relative to SEQ ID NO: 6 that are associated with the improved enzymatic property. Techniques and methods for deriving further engineered polypeptides are known in the art and include the methods of directed evolution as described herein.

The present disclosure contemplates that any of the exemplary engineered polypeptides of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206 can be used as the starting amino acid sequence (i.e., the “backbone” sequence) for subsequent rounds of evolution in which a library of genes having encoding additional amino acid differences in the backbone (e.g., adding in new combinations of various amino acid differences from other polypeptides in Tables 2A, 2B, 2C, and 2D) is synthesized, expressed, and screened in high-throughput for particular improved properties (e.g., thermostability, total substrate conversion, stereoselectivity, etc.). The design of the libraries can be controlled such that only certain amino acid positions are allowed to change, while others are not. Thus, a backbone set of amino acid differences that are associated with improved properties can be maintained throughout the directed evolution process. The most improved engineered polypeptides from each round could then be used as the parent “backbone” sequence for subsequent rounds of evolution. The resulting engineered transaminase polypeptides having further improvements in its properties will retain some or all of the starting backbone amino acid differences and include new amino acid differences, typically while retaining an overall sequence identity to the starting backbone of at least 80%. It is contemplated, however, that one or more of the backbone amino acid differences can be changed during the directed evolution process leading to further improved properties in the engineered polypeptides. Further improvements at later rounds of evolution such as “fine tuning” an engineered polypeptide for certain process conditions (e.g., solvent conditions/concentrations, increased substrate and/or cofactor loading, pH, and temperature changes) may be generated by including amino acid differences at positions that had been maintained as unchanged throughout earlier rounds of evolution.

Accordingly, in some embodiments, the present disclosure provides engineered polypeptides capable of converting a racemic mixture of compound (1) to the R-amine products of compound (2a) and compound (2c) in at least 98% e.e. relative to the corresponding S-amine products of compound (2d) and (2b), respectively, and/or capable of producing the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, and comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference amino acid sequence selected from any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206. In some embodiments, the amino acid sequence includes one or more residue differences as compared to SEQ ID NO:6 at the following residue positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. In some embodiments, the amino acid sequence includes one or more residue differences as compared to SEQ ID NO:6 selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X69C; X69V; X69W; X94L; X99L; X108V; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X135Q; X136W; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X1565; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I.

In some embodiments, the engineered polypeptide capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions and comprising an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference amino acid sequence selected from any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, further comprises one or more combinations of amino acid differences as compared to SEQ ID NO: 6 selected from the following: (a) X124V, and X210S; (b) X124V, X136W, and X210S; (c) X69V, and X136W; (d) X69V, and X215Y; (e) X69V, and X217S; (f) X69V, X124I, and X136W; (g) X69V; X136W, and X257F; (h) X44V, and X223N; (i) X56S, X69V, X136W, and X265T; (j) X28P, X69V, and X136W; and X69V, X124I, X136W, and X215F. In some embodiments, in addition to one or more of the above combinations, the engineered polypeptide amino acid sequence further comprises one or more amino acid residue differences as compared to SEQ ID NO: 6 selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X54K; X54N; X54P; X54R; X56G; X94L; X124I; X126A; X126T; X150A; X150N; X156S; X215F; and X267V.

In some embodiments, the engineered polypeptide capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions and comprising an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference amino acid sequence selected from any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, comprises an amino acid difference as compared to SEQ ID NO: 6 at one or more of the following positions: X28; X69; X124; X126; X136; X150; X156; X199; X209; X215; X217; and X223; and further comprises an amino acid difference as compared to SEQ ID NO: 6 at one or more of the following positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X94; X99; X108; X126; X135; X141; X142; X155; X157; X164; X165; X171; X182; X210; X213; X218; X245; X257; X265; X267; X296; and X328. In some embodiments, the amino acid differences as compared to SEQ ID NO: 6 at positions X28; X69; X124; X126; X136; X150; X156; X199; X209; X215; X217; and/or X223, are selected from the following: X28P; X69C; X69V; X69W; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X136W; X150A; X150N; X156S; X199F; X199R; X199Y; X209C; X209D; X209E; X215F; X215Y; X217S; X223I; X223L; X223M; and X223N. In some embodiments, the amino acid differences as compared to SEQ ID NO: 6 at positions X28; X69; X124; X126; X136; X150; X156; X199; X209; X215; X217; and/or X223 are selected from the following: X28P; X69C; X136W; X150N; X156S; X199F; X199Y; and X217S. In some embodiments, the amino acid differences as compared to SEQ ID NO: 6 at positions X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X94; X99; X108; X135; X141; X142; X155; X157; X164; X165; X171; X182; X210; X213; X218; X245; X257; X265; X267; X296; and X328 are selected from: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X94L; X99L; X108V; X135Q; X141L; X142R; X142T; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X210S; X213P; X218M; X245S; X257F; X265T; X267V; X296S; and X328I.

As mentioned above, the polypeptide sequence of SEQ ID NO: 6 used as the starting backbone for the generation of the exemplary engineered transaminase polypeptides is also an engineered transaminase polypeptide having the following 24 amino acid differences relative to the naturally occurring transaminase of Arthrobacter sp. KNK168 (SEQ ID NO: 2): S8P; Y60F; L61Y; H62T; V65A; V69T; D81G; M94I; 196L; F122I; G136F; A169L; V1991; A209L; G215C; G217N; S223P; L269P; L273Y; T282S; A284G; P297S; I306V; and S321P. Thus, in some embodiments, the engineered polypeptide capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions and comprising an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference amino acid sequence selected from any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, further comprises a polypeptide amino acid sequence that does not include an amino acid difference as compared to SEQ ID NO: 6 at one or more of the following positions: X8; X60; X61; X62; X65; X81; X94; X96; X122; X169; X269; X273; X282; X284; X297; X306; and X321. In some embodiments, the amino acid sequence that does not include an amino acid difference as compared to SEQ ID NO: 6 at any of the following positions: X8; X60; X61; X62; X65; X81; X94; X96; X122; X169; X269; X273; X282; X284; X297; X306; and X321.

In some embodiments, the present disclosure provides a non-naturally occurring polypeptide capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, and further comprises the set of one or more amino acid residue differences as compared to SEQ ID NO:6 found in any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206.

In addition to the residue positions specified above, any of the engineered transaminase polypeptides disclosed herein can further comprise other residue differences relative to the reference polypeptide sequence of SEQ ID NO: 6 at other residue positions i.e., residue positions other than X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. Residue differences at these other residue positions provide for additional variations in the amino acid sequence without altering the polypeptide's ability to convert a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions. Accordingly, in some embodiments, in addition to the set of amino acid residue differences of any one of the engineered transaminase polypeptides of any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, the sequence can further comprise one or several residue differences at other amino acid residue positions as compared to the SEQ ID NO: 6, or 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-11, 1-12, 1-14, 1-15, 1-16, 1-18, 1-20, 1-22, 1-24, 1-26, 1-30, 1-35, 1-40 residue differences at other amino acid residue positions as compared to the SEQ ID NO: 6. In some embodiments, the number of differences as compared to the reference sequence can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, 50, 55, or 60 residue positions. In some embodiments, the residue differences at other amino acid residue positions can comprise conservative substitutions and/or non-conservative substitutions as compared to a reference polypeptide of the wild-type polypeptide of SEQ ID NO: 2 or the engineered polypeptides of SEQ ID NO: 4 or 6.

Amino acid residue differences at other positions relative to the wild-type sequence of SEQ ID NO: 2 and the affect of these differences on enzyme function are provide by other engineered transaminase polypeptides disclosed in U.S. application Ser. No. 12/714,397, filed Feb. 26, 2010, which is hereby incorporated by reference herein. Accordingly, in some embodiments, one or more of the amino acid differences as compared to the wild-type sequence of SEQ ID NO: 2, provided in the engineered transaminase polypeptide amino acid sequences of U.S. application Ser. No. 12/714,397, filed Feb. 26, 2010 (see e.g., Table 2 of U.S. application Ser. No. 12/714,397), could also be introduced into a engineered transaminase polypeptide of the present disclosure. In some embodiments, any of the engineered polypeptide disclosed herein can comprise an amino acid sequence with the further proviso that the sequence does not comprise an amino acid residue differences as compared to SEQ ID NO: 6 at one or more of the following positions: X28; X69; X124; X126; X136; X150; X156; X199; X209; X215; X217; and X223. In some embodiments, any of the engineered polypeptide disclosed herein can comprise an amino acid sequence with the further proviso that the sequence does not comprise one or more amino acid residue differences as compared to SEQ ID NO: 6 selected from the following: X28P; X69C; X136W; X150N; X156S; X199F; X199Y; and X217S.

In some embodiments, the present disclosure also provides engineered transaminase polypeptides that comprise a fragment of any of the engineered transaminase polypeptides described herein that retains the functional activity and/or improved property of that engineered transaminase. Accordingly, in some embodiments, the present disclosure provides a polypeptide fragment capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, wherein the fragment comprises at least about 80%, 90%, 95%, 98%, or 99% of a full-length amino acid sequence of a engineered transaminase polypeptide of the present disclosure, such as an exemplary engineered polypeptide of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206.

In some embodiments, the provides an engineered transaminase polypeptide having an amino acid sequence comprising a deletion as compared to any one of the engineered transaminase polypeptides described herein, such as the exemplary engineered polypeptides of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206. Thus, for each and every embodiment of the engineered transaminase polypeptides of the disclosure, the amino acid sequence can comprise deletions of one or more amino acids, 2 or more amino acids, 3 or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 or more amino acids, 8 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, up to 10% of the total number of amino acids, up to 10% of the total number of amino acids, up to 20% of the total number of amino acids, or up to 30% of the total number of amino acids of the transaminase polypeptides, where the associated functional activity and/or improved properties of the engineered transaminase described herein is maintained. In some embodiments, the deletions can comprise, 1-2, 1-3, 1-4, 1-5, 1-6, 1-7, 1-8, 1-9, 1-10, 1-15, 1-20, 1-21, 1-22, 1-23, 1-24, 1-25, 1-30, 1-35, 1-40, 1-45, 1-50, 1-55, or 1-60 amino acid residues. In some embodiments, the number of deletions can be 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 30, 30, 35, 40, 45, 50, 55, or 60 amino acids. In some embodiments, the deletions can comprise deletions of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 20, 21, 22, 23, 24, 25 or 30 amino acid residues.

In some embodiments, the provides an engineered transaminase polypeptide having an amino acid sequence comprising an insertion as compared to any one of the engineered transaminase polypeptides described herein, such as the exemplary engineered polypeptides of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206. Thus, for each and every embodiment of the transaminase polypeptides of the disclosure, the insertions can comprise one or more amino acids, 2 or more amino acids, 3 or more amino acids, 4 or more amino acids, 5 or more amino acids, 6 or more amino acids, 8 or more amino acids, 10 or more amino acids, 15 or more amino acids, or 20 or more amino acids, where the associated functional activity and/or improved properties of the engineered transaminase described herein is maintained. The insertions can be to amino or carboxy terminus of the transaminase, or internal portions of the transaminase polypeptide.

In some embodiments, the present disclosure provides a non-naturally occurring polypeptide capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, which comprises an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to SEQ ID NO: 6, with the proviso that the amino acid sequence is not identical to any one or more of the engineered transaminase polypeptides amino acid sequences disclosed in U.S. application Ser. No. 12/714,397, filed Feb. 26, 2010.

In some embodiments, the polypeptides of the disclosure can be in the form of fusion polypeptides in which the engineered polypeptides are fused to other polypeptides, such as, by way of example and not limitation, antibody tags (e.g., myc epitope), purification sequences (e.g., His tags for binding to metals), and cell localization signals (e.g., secretion signals). Thus, the engineered polypeptides described herein can be used with or without fusions to other polypeptides.

The engineered transaminase polypeptides described herein are not restricted to the genetically encoded amino acids. In addition to the genetically encoded amino acids, the polypeptides described herein may be comprised, either in whole or in part, of naturally-occurring and/or synthetic non-encoded amino acids. Certain commonly encountered non-encoded amino acids of which the polypeptides described herein may be comprised include, but are not limited to: the D-stereomers of the genetically-encoded amino acids; 2,3-diaminopropionic acid (Dpr); α-aminoisobutyric acid (Aib); c-aminohexanoic acid (Aha); δ-aminovaleric acid (Ava); N-methylglycine or sarcosine (MeGly or Sar); ornithine (Orn); citrulline (Cit); t-butylalanine (Bua); t-butylglycine (Bug); N-methylisoleucine (MeIle); phenylglycine (Phg); cyclohexylalanine (Cha); norleucine (Nle); naphthylalanine (NaI); 2-chlorophenylalanine (Ocf); 3-chlorophenylalanine (Mcf); 4-chlorophenylalanine (Pcf); 2-fluorophenylalanine (Off); 3-fluorophenylalanine (Mff); 4-fluorophenylalanine (Pff); 2-bromophenylalanine (Obf); 3-bromophenylalanine (Mbf); 4-bromophenylalanine (Pbf); 2-methylphenylalanine (Omf); 3-methylphenylalanine (Mmf); 4-methylphenylalanine (Pmf); 2-nitrophenylalanine (Onf); 3-nitrophenylalanine (Mnf); 4-nitrophenylalanine (Pnf); 2-cyanophenylalanine (Ocf); 3-cyanophenylalanine (Mcf); 4-cyanophenylalanine (Pcf); 2-trifluoromethylphenylalanine (Otf); 3-trifluoromethylphenylalanine (Mtf); 4-trifluoromethylphenylalanine (Ptf); 4-aminophenylalanine (Paf); 4-iodophenylalanine (Pif); 4-aminomethylphenylalanine (Pamf); 2,4-dichlorophenylalanine (Opef); 3,4-dichlorophenylalanine (Mpcf); 2,4-difluorophenylalanine (Opff); 3,4-difluorophenylalanine (Mpff); pyrid-2-ylalanine (2pAla); pyrid-3-ylalanine (3pAla); pyrid-4-ylalanine (4pAla); naphth-1-ylalanine (1nAla); naphth-2-ylalanine (2nAla); thiazolylalanine (taAla); benzothienylalanine (bAla); thienylalanine (tAla); furylalanine (fAla); homophenylalanine (hPhe); homotyrosine (hTyr); homotryptophan (hTrp); pentafluorophenylalanine (5ff); styrylkalanine (sAla); authrylalanine (aAla); 3,3-diphenylalanine (Dfa); 3-amino-5-phenypentanoic acid (Afp); penicillamine (Pen); 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic); β-2-thienylalanine (Thi); methionine sulfoxide (Mso); N(w)-nitroarginine (nArg); homolysine (hLys); phosphonomethylphenylalanine (pmPhe); phosphoserine (pSer); phosphothreonine (pThr); homoaspartic acid (hAsp); homoglutanic acid (hGlu); 1-aminocyclopent-(2 or 3)-ene-4 carboxylic acid; pipecolic acid (PA), azetidine-3-carboxylic acid (ACA); 1-aminocyclopentane-3-carboxylic acid; allylglycine (aOly); propargylglycine (pgGly); homoalanine (hAla); norvaline (nVal); homoleucine (hLeu), homovaline (hVal); homoisolencine (hIle); homoarginine (hArg); N-acetyl lysine (AcLys); 2,4-diaminobutyric acid (Dbu); 2,3-diaminobutyric acid (Dab); N-methylvaline (MeVal); homocysteine (hCys); homoserine (hSer); hydroxyproline (Hyp) and homoproline (hPro). Additional non-encoded amino acids of which the polypeptides described herein may be comprised will be apparent to those of skill in the art (see, e.g., the various amino acids provided in Fasman, 1989, CRC Practical Handbook of Biochemistry and Molecular Biology, CRC Press, Boca Raton, Fla., at pp. 3-70 and the references cited therein, all of which are incorporated by reference). These amino acids may be in either the L- or D-configuration.

Those of skill in the art will recognize that amino acids or residues bearing side chain protecting groups may also comprise the polypeptides described herein. Non-limiting examples of such protected amino acids, which in this case belong to the aromatic category, include (protecting groups listed in parentheses), but are not limited to: Arg(tos), Cys(methylbenzyl), Cys (nitropyridinesulfenyl), Glu(δ-benzylester), Gln(xanthyl), Asn(N-δ-xanthyl), His(bom), His(benzyl), His(tos), Lys(fmoc), Lys(tos), Ser(O-benzyl), Thr (O-benzyl) and Tyr(O-benzyl).

Non-encoding amino acids that are conformationally constrained of which the polypeptides described herein may be composed include, but are not limited to, N-methyl amino acids (L-configuration); 1-aminocyclopent-(2 or 3)-ene-4-carboxylic acid; pipecolic acid; azetidine-3-carboxylic acid; homoproline (hPro); and 1-aminocyclopentane-3-carboxylic acid.

As described above the various modifications introduced into the naturally occurring polypeptide to generate an engineered transaminase enzyme can be targeted to a specific property of the enzyme.

In some embodiments, the engineered polypeptides described herein can be provided in the form of kits. The polypeptides in the kits may be present individually or as a plurality of polypeptides. The kits can further include reagents for carrying out enzymatic reactions, substrates for assessing the activity of polypeptides, as well as reagents for detecting the products. The kits can also include reagent dispensers and instructions for use of the kits.

In some embodiments, the engineered polypeptides can be provided on a solid substrate. In some embodiments, the polypeptides can be provided in the form of an array in which the polypeptides are arranged in positionally distinct locations. The array can be used to test a variety of substrate compounds for conversion by the polypeptides. “Substrate,” “support,” “solid support,” “solid carrier,” or “resin” in the context of arrays refer to any solid phase material. Substrate also encompasses terms such as “solid phase,” “surface,” and/or “membrane.” A solid support can be composed of organic polymers such as polystyrene, polyethylene, polypropylene, polyfluoroethylene, polyethyleneoxy, and polyacrylamide, as well as co-polymers and grafts thereof. A solid support can also be inorganic, such as glass, silica, controlled pore glass (CPG), reverse phase silica or metal, such as gold or platinum. The configuration of a substrate can be in the form of beads, spheres, particles, granules, a gel, a membrane or a surface. Surfaces can be planar, substantially planar, or non-planar. Solid supports can be porous or non-porous, and can have swelling or non-swelling characteristics. A solid support can be configured in the form of a well, depression, or other container, vessel, feature, or location. A plurality of supports can be configured on an array at various locations, addressable for robotic delivery of reagents, or by detection methods and/or instruments.

In certain embodiments, the kits of the present disclosure include arrays comprising a plurality of different engineered transaminase polypeptides at different addressable position, wherein the different polypeptides are different variants of a reference sequence each having at least one different improved enzyme property. Such arrays comprising a plurality of engineered polypeptides and methods of their use are described in, e.g., WO2009/008908A2.

In some embodiments, the transaminase polypeptides are bound to a substrate. The transaminase polypeptide can be bound non-covalently or covalently. Various methods for conjugation to substrates, e.g., membranes, beads, glass, etc. are described in, among others, Hermanson, G. T., Bioconjugate Techniques, Second Edition, Academic Press; (2008), and Bioconjugation Protocols Strategies and Methods, In Methods in Molecular Biology, C. M. Niemeyer ed., Humana Press (2004); the disclosures of which are incorporated herein by reference.

5.4 Polynucleotides, Control Sequences, Expression Vectors, and Host Cells Useful for Preparing Engineered Transaminase Polypeptides

In another aspect, the present disclosure provides polynucleotides encoding the engineered transaminase polypeptides described herein. The polynucleotides may be operatively linked to one or more heterologous regulatory sequences that control gene expression to create a recombinant polynucleotide capable of expressing the polypeptide. Expression constructs containing a heterologous polynucleotide encoding the engineered transaminase can be introduced into appropriate host cells to express the corresponding transaminase polypeptide.

Because of the knowledge of the codons corresponding to the various amino acids, availability of a protein sequence provides a description of all the polynucleotides capable of encoding the subject. The degeneracy of the genetic code, where the same amino acids are encoded by alternative or synonymous codons allows an extremely large number of nucleic acids to be made, all of which encode the improved transaminase enzymes disclosed herein. Thus, having identified a particular amino acid sequence, those skilled in the art could make any number of different nucleic acids by simply modifying the sequence of one or more codons in a way which does not change the amino acid sequence of the protein. In this regard, the present disclosure specifically contemplates each and every possible variation of polynucleotides that could be made by selecting combinations based on the possible codon choices, and all such variations are to be considered specifically disclosed for any polypeptide disclosed herein, including the amino acid sequences of the exemplary engineered polypeptides summarized in Tables 2A, 2B, 2C, and 2D and disclosed in the sequence listing incorporated by reference herein as SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206.

In various embodiments, the codons are preferably selected to fit the host cell in which the protein is being produced. For example, preferred codons used in bacteria are used to express the gene in bacteria; preferred codons used in yeast are used for expression in yeast; and preferred codons used in mammals are used for expression in mammalian cells.

In certain embodiments, all codons need not be replaced to optimize the codon usage of the transaminases since the natural sequence will comprise preferred codons and because use of preferred codons may not be required for all amino acid residues. Consequently, codon optimized polynucleotides encoding the transaminase enzymes may contain preferred codons at about 40%, 50%, 60%, 70%, 80%, or greater than 90% of codon positions of the full length coding region.

In some embodiments, the polynucleotide encodes a transaminase polypeptide comprising an amino acid sequence that is at least about 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99%, or more identical to the reference sequence of SEQ ID NO:6, where the polypeptide has transaminase activity and one or more of the improved properties as compared described herein, for example the ability to convert a racemic mixture of compound (1) to the R-amine products of compound (2a) and compound (2c) in at least 98% e.e. relative to the corresponding S-amine products of compound (2d) and (2b), respectively, and producing the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions. In some embodiments, the polynucleotide encodes an engineered transaminase polypeptide comprises an amino acid sequence that has the percent identity described above and has one or more amino acid residue differences as compared to SEQ ID NO: 6 at one or more amino acid residue positions selected from the following: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328.

In some embodiments, the polynucleotide comprises a nucleotide sequence encoding an engineered transaminase polypeptide with an amino acid sequence that has at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity to any of the engineered transaminase polypeptides disclosed herein. Accordingly, in some embodiments, the polynucleotide encodes an amino acid sequence that is at least about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or more identical to SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, where the polypeptide is capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions. In some embodiments, the polynucleotide encodes an engineered transaminase polypeptide comprises an amino acid sequence that has the percent identity described above and has one or more amino acid residue differences as compared to a reference polypeptide of SEQ ID NO: 2, 4, or 6 at one or more amino acid residue positions selected from the following: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328.

In some embodiments, the polynucleotides encoding the engineered transaminases are selected from SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, and 205.

In some embodiments, the present disclosure provides polynucleotides are capable of hybridizing under highly stringent conditions to a polynucleotide selected from SEQ ID NO: 3, 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, or 101, or a complement thereof, and encodes a polypeptide having transaminase activity with one or more of the improved properties described herein. In some embodiments, the polynucleotide capable of hybridizing under highly stringent conditions encodes a transaminase polypeptide comprising an amino acid sequence that has one or more amino acid residue differences as compared to a reference polypeptide of SEQ ID NO: 2, 4, or 6, at one or more amino acid residue positions selected from the following: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328.

In some embodiments, the polynucleotides encode the polypeptides described herein but have about 80% or more sequence identity, about 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% or more sequence identity at the nucleotide level to a reference polynucleotide encoding the engineered transaminase polypeptide. In some embodiments, the reference polynucleotide sequence is selected from SEQ ID NO: 5, 7, 9, 11, 13, 15, 17, 19, 21, 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 69, 71, 73, 75, 77, 79, 81, 83, 85, 87, 89, 91, 93, 95, 97, 99, 101, 103, 105, 107, 109, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 139, 141, 143, 145, 147, 149, 151, 153, 155, 157, 159, 161, 163, 165, 167, 169, 171, 173, 175, 177, 179, 181, 183, 185, 187, 189, 191, 193, 195, 197, 199, 201, 203, and 205.

An isolated polynucleotide encoding an engineered transaminase polypeptide may be manipulated in a variety of ways to provide for expression of the polypeptide, including further sequence alteration by codon-optimization to improve expression, insertion in a suitable expression with or without further control sequences, and transformation into a host cell suitable for expression and production of the polypeptide.

Manipulation of the isolated polynucleotide prior to its insertion into a vector may be desirable or necessary depending on the expression vector. The techniques for modifying polynucleotides and nucleic acid sequences utilizing recombinant DNA methods are well known in the art. Guidance is provided in Sambrook et al., 2001, Molecular Cloning: A Laboratory Manual, 3^(rd) Ed., Cold Spring Harbor Laboratory Press; and Current Protocols in Molecular Biology, Ausubel. F. ed., Greene Pub. Associates, 1998, updates to 2006.

The polynucleotides disclosed herein can further comprise a promoter sequence depending on the particular cellular production system used. For bacterial host cells, suitable promoters for directing transcription of the nucleic acid constructs of the present disclosure, include the promoters obtained from the E. coli lac operon, Streptomyces coelicolor agarase gene (dagA), Bacillus subtilis levansucrase gene (sacB), Bacillus licheniformis alpha-amylase gene (amyL), Bacillus stearothermophilus maltogenic amylase gene (amyM), Bacillus amyloliquefaciens alpha-amylase gene (amyQ), Bacillus licheniformis penicillinase gene (penP), Bacillus subtilis xylA and xylB genes, and prokaryotic beta-lactamase gene (VIIIa-Kamaroff et al., 1978, Proc. Natl. Acad. Sci. USA 75: 3727-3731), as well as the tac promoter (DeBoer et al., 1983, Proc. Natl. Acad. Sci. USA 80: 21-25). For filamentous fungal host cells, suitable promoters for directing the transcription of the nucleic acid constructs of the present disclosure include promoters obtained from the genes for Aspergillus oryzae TAKA amylase, Rhizomucor miehei aspartic proteinase, Aspergillus niger neutral alpha-amylase, Aspergillus niger acid stable alpha-amylase, Aspergillus niger or Aspergillus awamori glucoamylase (glaA), Rhizomucor miehei lipase, Aspergillus oryzae alkaline protease, Aspergillus oryzae triose phosphate isomerase, Aspergillus nidulans acetamidase, and Fusarium oxysporum trypsin-like protease (WO 96/00787), as well as the NA2-tpi promoter (a hybrid of the promoters from the genes for Aspergillus niger neutral alpha-amylase and Aspergillus oryzae triose phosphate isomerase), and mutant, truncated, and hybrid promoters thereof. In a yeast host, useful promoters can be from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae galactokinase (GAL1), Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP), and Saccharomyces cerevisiae 3-phosphoglycerate kinase. Other useful promoters for yeast host cells are described by Romanos et al., 1992, Yeast 8:423-488.

The control sequence may also be a suitable transcription terminator sequence, a sequence recognized by a host cell to terminate transcription. The terminator sequence is operably linked to the 3′ terminus of the nucleic acid sequence encoding the polypeptide. Any terminator which is functional in the host cell of choice may be used in the present disclosure. For example, exemplary transcription terminators for filamentous fungal host cells can be obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Aspergillus niger alpha-glucosidase, and Fusarium oxysporum trypsin-like protease. Exemplary terminators for yeast host cells can be obtained from the genes for Saccharomyces cerevisiae enolase, Saccharomyces cerevisiae cytochrome C(CYC1), and Saccharomyces cerevisiae glyceraldehyde-3-phosphate dehydrogenase. Other useful terminators for yeast host cells are described by Romanos et al., 1992, supra.

The control sequence may also be a suitable leader sequence, a non-translated region of an mRNA that is important for translation by the host cell. The leader sequence is operably linked to the 5′ terminus of the nucleic acid sequence encoding the polypeptide. Any leader sequence that is functional in the host cell of choice may be used. Exemplary leaders for filamentous fungal host cells are obtained from the genes for Aspergillus oryzae TAKA amylase and Aspergillus nidulans triose phosphate isomerase. Suitable leaders for yeast host cells are obtained from the genes for Saccharomyces cerevisiae enolase (ENO-1), Saccharomyces cerevisiae 3-phosphoglycerate kinase, Saccharomyces cerevisiae alpha-factor, and Saccharomyces cerevisiae alcohol dehydrogenase/glyceraldehyde-3-phosphate dehydrogenase (ADH2/GAP).

The control sequence may also be a polyadenylation sequence, a sequence operably linked to the 3′ terminus of the nucleic acid sequence and which, when transcribed, is recognized by the host cell as a signal to add polyadenosine residues to transcribed mRNA. Any polyadenylation sequence which is functional in the host cell of choice may be used in the present disclosure. Exemplary polyadenylation sequences for filamentous fungal host cells can be from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger glucoamylase, Aspergillus nidulans anthranilate synthase, Fusarium oxysporum trypsin-like protease, and Aspergillus niger alpha-glucosidase. Useful polyadenylation sequences for yeast host cells are described by Guo and Sherman, 1995, Mol Cell Bio 15:5983-5990.

The control sequence may also be a signal peptide coding region that codes for an amino acid sequence linked to the amino terminus of a polypeptide and directs the encoded polypeptide into the cell's secretory pathway. The 5′ end of the coding sequence of the nucleic acid sequence may inherently contain a signal peptide coding region naturally linked in translation reading frame with the segment of the coding region that encodes the secreted polypeptide. Alternatively, the 5′ end of the coding sequence may contain a signal peptide coding region that is foreign to the coding sequence. The foreign signal peptide coding region may be required where the coding sequence does not naturally contain a signal peptide coding region.

Alternatively, the foreign signal peptide coding region may simply replace the natural signal peptide coding region in order to enhance secretion of the polypeptide. However, any signal peptide coding region which directs the expressed polypeptide into the secretory pathway of a host cell of choice may be used in the present disclosure. Effective signal peptide coding regions for bacterial host cells are the signal peptide coding regions obtained from the genes for Bacillus NC1B 11837 maltogenic amylase, Bacillus stearothermophilus alpha-amylase, Bacillus licheniformis subtilisin, Bacillus licheniformis beta-lactamase, Bacillus stearothermophilus neutral proteases (nprT, nprS, nprM), and Bacillus subtilis prsA. Further signal peptides are described by Simonen and Palva, 1993, Microbiol Rev 57: 109-137. Effective signal peptide coding regions for filamentous fungal host cells can be the signal peptide coding regions obtained from the genes for Aspergillus oryzae TAKA amylase, Aspergillus niger neutral amylase, Aspergillus niger glucoamylase, Rhizomucor miehei aspartic proteinase, Humicola insolens cellulase, and Humicola lanuginosa lipase. Useful signal peptides for yeast host cells can be from the genes for Saccharomyces cerevisiae alpha-factor and Saccharomyces cerevisiae invertase. Other useful signal peptide coding regions are described by Romanos et al., 1992, supra.

The control sequence may also be a propeptide coding region that codes for an amino acid sequence positioned at the amino terminus of a polypeptide. The resultant polypeptide is known as a pro-enzyme or pro-polypeptide (or a zymogen in some cases). A pro-polypeptide can be converted to a mature active polypeptide by catalytic or autocatalytic cleavage of the pro-peptide from the pro-polypeptide. The pro-peptide coding region may be obtained from the genes for Bacillus subtilis alkaline protease (aprE), Bacillus subtilis neutral protease (nprT), Saccharomyces cerevisiae alpha-factor, Rhizomucor miehei aspartic proteinase, and Myceliophthora thermophila lactase (WO 95/33836). Where both signal peptide and propeptide regions are present at the amino terminus of a polypeptide, the pro-peptide region is positioned next to the amino terminus of a polypeptide and the signal peptide region is positioned next to the amino terminus of the pro-peptide region.

It may also be desirable to add regulatory sequences, which allow the regulation of the expression of the polypeptide relative to the growth of the host cell. Examples of regulatory systems are those which cause the expression of the gene to be turned on or off in response to a chemical or physical stimulus, including the presence of a regulatory compound. In prokaryotic host cells, suitable regulatory sequences include the lac, tac, and trp operator systems. In yeast host cells, suitable regulatory systems include, as examples, the ADH2 system or GAL1 system. In filamentous fungi, suitable regulatory sequences include the TAKA alpha-amylase promoter, Aspergillus niger glucoamylase promoter, and Aspergillus oryzae glucoamylase promoter. Other examples of regulatory sequences are those which allow for gene amplification. In eukaryotic systems, these include the dihydrofolate reductase gene, which is amplified in the presence of methotrexate, and the metallothionein genes, which are amplified with heavy metals. In these cases, the nucleic acid sequence encoding the polypeptide of the present disclosure would be operably linked with the regulatory sequence.

In another aspect, the present disclosure is also directed to a recombinant expression vector comprising a polynucleotide encoding an engineered transaminase polypeptide or a variant thereof, and one or more expression regulating regions such as a promoter and a terminator, a replication origin, etc., depending on the type of hosts into which they are to be introduced. The various nucleic acid and control sequences described above may be joined together to produce a recombinant expression vector which may include one or more convenient restriction sites to allow for insertion or substitution of the nucleic acid sequence encoding the polypeptide at such sites. Alternatively, the nucleic acid sequence of the present disclosure may be expressed by inserting the nucleic acid sequence or a nucleic acid construct comprising the sequence into an appropriate vector for expression. In creating the expression vector, the coding sequence is located in the vector so that the coding sequence is operably linked with the appropriate control sequences for expression.

The recombinant expression vector may be any vector (e.g., a plasmid or virus), which can be conveniently subjected to recombinant DNA procedures and can bring about the expression of the polynucleotide sequence. The choice of the vector will typically depend on the compatibility of the vector with the host cell into which the vector is to be introduced. The vectors may be linear or closed circular plasmids. The expression vector may be an autonomously replicating vector, i.e., a vector that exists as an extrachromosomal entity, the replication of which is independent of chromosomal replication, e.g., a plasmid, an extrachromosomal element, a minichromosome, or an artificial chromosome. The vector may contain any means for assuring self-replication. Alternatively, the vector may be one which, when introduced into the host cell, is integrated into the genome and replicated together with the chromosome(s) into which it has been integrated. Furthermore, a single vector or plasmid or two or more vectors or plasmids which together contain the total DNA to be introduced into the genome of the host cell, or a transposon may be used.

The expression vector of the present disclosure can include one or more selectable markers, which permit easy selection of transformed cells. A selectable marker is a gene the product of which provides for biocide or viral resistance, resistance to heavy metals, prototrophy to auxotrophs, and the like. Examples of bacterial selectable markers are the dal genes from Bacillus subtilis or Bacillus licheniformis, or markers, which confer antibiotic resistance such as ampicillin, kanamycin, chloramphenicol, or tetracycline resistance. Suitable markers for yeast host cells are ADE2, HIS3, LEU2, LYS2, MET3, TRP1, and URA3. Selectable markers for use in a filamentous fungal host cell include, but are not limited to, amdS (acetamidase), argB (ornithine carbamoyltransferase), bar (phosphinothricin acetyltransferase), hph (hygromycin phosphotransferase), niaD (nitrate reductase), pyrG (orotidine-5′-phosphate decarboxylase), sC (sulfate adenyltransferase), and trpC (anthranilate synthase), as well as equivalents thereof. Embodiments for use in an Aspergillus cell include the amdS and pyrG genes of Aspergillus nidulans or Aspergillus oryzae and the bar gene of Streptomyces hygroscopicus.

The expression vectors of the present disclosure also can include an element(s) that permits integration of the vector into the host cell's genome or autonomous replication of the vector in the cell independent of the genome. For integration into the host cell genome, the vector may rely on the nucleic acid sequence encoding the polypeptide or any other element of the vector for integration of the vector into the genome by homologous or non-homologous recombination.

Alternatively, the expression vector may contain additional nucleic acid sequences for directing integration by homologous recombination into the genome of the host cell. The additional nucleic acid sequences enable the vector to be integrated into the host cell genome at a precise location(s) in the chromosome(s). To increase the likelihood of integration at a precise location, the integrational elements should preferably contain a sufficient number of nucleic acids, such as 100 to 10,000 base pairs, preferably 400 to 10,000 base pairs, and most preferably 800 to 10,000 base pairs, which are highly homologous with the corresponding target sequence to enhance the probability of homologous recombination. The integrational elements may be any sequence that is homologous with the target sequence in the genome of the host cell. Furthermore, the integrational elements may be non-encoding or encoding nucleic acid sequences. On the other hand, the vector may be integrated into the genome of the host cell by non-homologous recombination.

For autonomous replication, the vector may further comprise an origin of replication enabling the vector to replicate autonomously in the host cell in question. Examples of bacterial origins of replication are P15A on or the origins of replication of plasmids pBR322, pUC19, pACYC177 (which plasmid has the P15A ori), or pACYC184 permitting replication in E. coli, and pUB110, pE194, pTA1060, or pAMβ1 permitting replication in Bacillus. Examples of origins of replication for use in a yeast host cell are the 2 micron origin of replication, ARS1, ARS4, the combination of ARS1 and CEN3, and the combination of ARS4 and CEN6. The origin of replication may be one having a mutation which makes its functioning temperature-sensitive in the host cell (see, e.g., Ehrlich, 1978, Proc Natl Acad Sci. USA 75:1433).

More than one copy of a nucleic acid sequence of the present disclosure may be inserted into the host cell to increase production of the gene product. An increase in the copy number of the nucleic acid sequence can be obtained by integrating at least one additional copy of the sequence into the host cell genome or by including an amplifiable selectable marker gene with the nucleic acid sequence where cells containing amplified copies of the selectable marker gene, and thereby additional copies of the nucleic acid sequence, can be selected for by cultivating the cells in the presence of the appropriate selectable agent.

Many expression vectors useful with the embodiments of the present disclosure are commercially available. Suitable commercial expression vectors include p3xFLAGTM™ expression vectors from Sigma-Aldrich Chemicals, St. Louis Mo., which includes a CMV promoter and hGH polyadenylation site for expression in mammalian host cells and a pBR322 origin of replication and ampicillin resistance markers for amplification in E. coli. Other suitable expression vectors are pBluescriptll SK(−) and pBK-CMV, which are commercially available from Stratagene, LaJolla Calif., and plasmids which are derived from pBR322 (Gibco BRL), pUC (Gibco BRL), pREP4, pCEP4 (Invitrogen) or pPoly (Lathe et al., 1987, Gene 57:193-201).

In another aspect, the present disclosure provides a host cell comprising a polynucleotide encoding an improved transaminase polypeptide of the present disclosure, the polynucleotide being operatively linked to one or more control sequences for expression of the transaminase enzyme in the host cell. Host cells for use in expressing the polypeptides encoded by the expression vectors of the present disclosure are well known in the art and include but are not limited to, bacterial cells, such as E. coli, Arthrobacter sp. KNK168, Streptomyces and Salmonella typhimurium cells; fungal cells, such as yeast cells (e.g., Saccharomyces cerevisiae or Pichia pastoris (ATCC Accession No. 201178)); insect cells such as Drosophila S2 and Spodoptera Sf9 cells; animal cells such as CHO, COS, BHK, 293, and Bowes melanoma cells; and plant cells. Appropriate culture mediums and growth conditions for the above-described host cells are well known in the art.

Polynucleotides for expression of the transaminase may be introduced into cells by various methods known in the art. Techniques include among others, electroporation, biolistic particle bombardment, liposome mediated transfection, calcium chloride transfection, and protoplast fusion. Various methods for introducing polynucleotides into cells will be apparent to the skilled artisan.

An exemplary host cell is Escherichia coli W3110 (AfhuA). The expression vector was created by operatively linking a polynucleotide encoding an improved transaminase into the plasmid pCK110900I operatively linked to the lac promoter under control of the lad repressor. The expression vector also contained the P15a origin of replication and the chloramphenicol resistance gene.

5.6 Methods of Generating Engineered Transaminase Polypeptides

In some embodiments, to make the improved polynucleotides and polypeptides of the present disclosure, the naturally-occurring transaminase enzyme that catalyzes the transamination reaction is obtained (or derived) from Arthrobacter sp. KNK168. In some embodiments, the parent polynucleotide sequence is codon optimized to enhance expression of the transaminase in a specified host cell. The parental polynucleotide sequence encoding the wild-type polypeptide of Arthrobacter sp. KNK168 has been described (see e.g., Iwasaki et al., Appl. Microbiol. Biotechnol., 2006, 69: 499-505). Preparation of engineered transaminases based on this parental sequence are also described in U.S. application Ser. No. 12/714,397, filed Feb. 26, 2010 and International application PCT/US2010/025685, filed Feb. 26, 2010.

The engineered transaminases can be obtained by subjecting the polynucleotide encoding the naturally occurring transaminase to mutagenesis and/or directed evolution methods, as discussed above. An exemplary directed evolution technique is mutagenesis and/or DNA shuffling as described in Stemmer, 1994, Proc Natl Acad Sci USA 91:10747-10751; WO 95/22625; WO 97/0078; WO 97/35966; WO 98/27230; WO 00/42651; WO 01/75767 and U.S. Pat. No. 6,537,746. Other directed evolution procedures that can be used include, among others, staggered extension process (StEP), in vitro recombination (Zhao et al., 1998, Nat. Biotechnol. 16:258-261), mutagenic PCR (Caldwell et al., 1994, PCR Methods Appl. 3:S136-S140), and cassette mutagenesis (Black et al., 1996, Proc Natl Acad Sci USA 93:3525-3529). Mutagenesis and directed evolution techniques useful for the purposes herein are also described in e.g., Ling, et al., 1997, Anal. Biochem. 254(2):157-78; Dale et al., 1996, “Oligonucleotide-directed random mutagenesis using the phosphorothioate method,” in Methods Mol. Biol. 57:369-74; Smith, 1985, Ann. Rev. Genet. 19:423-462; Botstein et al., 1985, Science 229:1193-1201; Carter, 1986, Biochem. J. 237:1-7; Kramer et al., 1984, Cell, 38:879-887; Wells et al., 1985, Gene 34:315-323; Minshull et al., 1999, Curr Opin Chem Biol 3:284-290; Christians et al., 1999, Nature Biotech 17:259-264; Crameri et al., 1998, Nature 391:288-291; Crameri et al., 1997, Nature Biotech 15:436-438; Zhang et al., 1997, Proc Natl Acad Sci USA 94:45-4-4509; Crameri et al., 1996, Nature Biotech 14:315-319; Stemmer, 1994, Nature 370:389-391; Stemmer, 1994, Proc Natl Acad Sci USA 91:10747-10751; PCT Publ. Nos. WO 95/22625, WO 97/0078, WO 97/35966, WO 98/27230, WO 00/42651, and WO 01/75767; and U.S. Pat. No. 6,537,746. All publications and patent are hereby incorporated by reference herein.

The clones obtained following mutagenesis treatment can be screened for engineered transaminases having a desired improved enzyme property. Measuring enzyme activity from the expression libraries can be performed using the standard biochemistry techniques, such as HPLC analysis following OPA derivatization of the product amine.

Where the improved enzyme property desired is thermostability, enzyme activity may be measured after subjecting the enzyme preparations to a defined temperature and measuring the amount of enzyme activity remaining after heat treatments. Clones containing a polynucleotide encoding a transaminase are then isolated, sequenced to identify the nucleotide sequence changes (if any), and used to express the enzyme in a host cell.

Where the sequence of the engineered polypeptide is known, the polynucleotides encoding the enzyme can be prepared by standard solid-phase methods, according to known synthetic methods. In some embodiments, fragments of up to about 100 bases can be individually synthesized, then joined (e.g., by enzymatic or chemical litigation methods, or polymerase mediated methods) to form any desired continuous sequence. For example, polynucleotides and oligonucleotides of the disclosure can be prepared by chemical synthesis using, e.g., the classical phosphoramidite method described by Beaucage et al., 1981, Tet Left 22:1859-69, or the method described by Matthes et al., 1984, EMBO J. 3:801-05, e.g., as it is typically practiced in automated synthetic methods. According to the phosphoramidite method, oligonucleotides are synthesized, e.g., in an automatic DNA synthesizer, purified, annealed, ligated and cloned in appropriate vectors. In addition, essentially any nucleic acid can be obtained from any of a variety of commercial sources.

In some embodiments, the present disclosure also provides methods for preparing or manufacturing the engineered transamination polypeptides capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, wherein the methods comprise: (a) culturing a host cell capable of expressing a polynucleotide encoding the engineered polypeptide; and (b) optionally isolating the polypeptide from the host cell. The engineered polypeptides can be expressed in appropriate cells (as described above), and isolated (or recovered) from the host cells and/or the culture medium using any one or more of the well known techniques used for protein purification, including, among others, lysozyme treatment, sonication, filtration, salting-out, ultra-centrifugation, and chromatography. Chromatographic techniques for isolation of the ketoreductase polypeptide include, among others, reverse phase chromatography high performance liquid chromatography, ion exchange chromatography, gel electrophoresis, and affinity chromatography. Conditions for purifying a particular engineered polypeptide will depend, in part, on factors such as net charge, hydrophobicity, hydrophilicity, molecular weight, molecular shape, etc., and will be apparent to those having skill in the art.

5.7 Methods of Using the Engineered Transaminase Enzymes and Compounds Prepared Therewith

In another aspect of the present disclosure, any of the engineered transaminase polypeptides disclosed herein capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions can be used in a method for the conversion of the substrate compound (1a), (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone, to the product of compound (2a), (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine. The method for preparing compound (2a) can comprise contacting compound (1a) with an engineered transaminase polypeptide of the present disclosure in the presence of an amino donor under suitable reaction conditions.

As described further below, and illustrated in the Examples, the present disclosure contemplates ranges of suitable reaction conditions that can be used in the method, including but not limited to ranges of pH, temperature, buffer, solvent system, substrate loading, mixture of substrate compound enantiomers (e.g., a racemic mixture), polypeptide loading, cofactor loading, atmosphere, and reaction time. Further suitable reaction conditions for carrying out the method for biocatalytic conversion of compound (1a) to compound (2a) using an engineered transaminase polypeptide described herein can be readily optimized by routine experimentation that includes, but is not limited to, contacting the engineered transaminase polypeptide and substrate (1a) under experimental reaction conditions of concentration, pH, temperature, solvent conditions, and detecting the production of compound (2a), for example, using the methods described in the Examples provided herein.

As described above, the engineered transaminase polypeptides of the present disclosure generally comprise an amino acid sequence having at least 80%, 85%, 86%, 87%, 88%, 89%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity to a reference amino acid sequence selected from any one of SEQ ID NO: 6, 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, and one or more residue differences as compared to SEQ ID NO:6 at the following residue positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. In various specific embodiments as disclosed above, the engineered polypeptide amino acid sequence includes one or more amino acid residue differences as compared to SEQ ID NO:6 selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X69C; X69V; X69W; X94L; X99L; X108V; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X135Q; X136W; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I.

The combination of improved enantioselectivity and diastereoselectivity of the engineered transaminase polypeptides of the present disclosure provides for a method capable of converting a racemic mixture of compound (1) to compound (2a) in a diastereomeric ratio relative to cis R-amine compound (2c) of at least about 2:1 and with high conversion yields (e.g., 85% or greater).

Accordingly, in some embodiments the high enantioselectivity for the R-amine products provides for a method wherein a mixture of compound (1a) and compound (1b) may be used and the method results in the R-amine products of compound (2a) and (2c) in an enantiomeric excess relative to the S-amine products of compound (2d) and (2b) of at least about 95% e.e., at least about 96% e.e., at least about 97% e.e., at least about 98% e.e., at least about 99% e.e., or at least about 99.9% e.e.

Similarly, the high diastereoselectivity for the trans R-amine product of compound (2a) provides for a method wherein a mixture of compound (1a) and compound (1b) may be used and the method results in the trans R-amine product of compound (2a) in a diastereomeric ratio relative to cis R-amine compound (2c) of at least about 2:1, at least about 3:1, at least about 4:1, at least about 8:1, at least about 10:1, at least about 15:1, at least about 20:1, or at least about 30:1.

In some embodiments, the engineered transaminase polypeptide is present at sufficient amounts to carry out the conversion of the substrate to product to the desired percent conversion of substrate to product in a defined time period under a defined process condition. In some embodiments, conversion yields of the product of compound (2a) generated in the reaction mixture are generally greater than about 50%, may also be greater than about 60%, may also be greater than about 70%, may also be greater than about 80%, may also be greater than 90%, and are often greater than about 97%.

The improved stereoselectivity and activity of the engineered transaminase polypeptides of the present disclosure in the conversion of compound (1a) to compound (2a) provides for methods wherein higher percentage conversion can be achieved with lower concentrations of the engineered polypeptide. The use of lower concentration of the engineered polypeptide in a method comprising a conversion of compound (1a) to compound (2a) also reduces the amount of residual protein that may need to be removed in subsequent steps for purification of compound (2a). In some embodiments of the method, the suitable reaction conditions comprise an engineered polypeptide concentration of about 0.1 to about 40 g/L, about 0.5 to about 20 g/L, about 1.0 to about 10 g/L, about 2 to about 5 g/L, about 40 g/L or less, about 20 g/L or less, about 15 g/L or less, about 10 g/L or less, about 5 g/L or less, about 3 g/L or less, about 2 g/L or less, about 1.5 g/L or less, about 1.0 g/L or less, about 0.75 g/L or less, or an even lower concentration.

In some embodiments of the method, the amino donor present comprises a compound selected from isopropylamine (also referred to herein as “IPM”), putrescine, L-lysine, α-phenethylamine, D-alanine, L-alanine, or D,L-alanine, or D,L-ornithine. In some embodiments, the amino donor is selected from the group consisting of IPM, putrescine, L-lysine, D- or L-alanine. In some embodiments, the amino donor is IPM. In some embodiments, the suitable reaction conditions comprise the amino donor present at a concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more.

Suitable reaction conditions for the methods of using the engineered transaminase polypeptides conversion of the substrate compound (1a) to the product of compound (2a) also typically comprise the presence of a cofactor in the reaction mixture comprising the engineered polypeptide contacting the substrate of compound (1a). =Cofactors useful in the methods using the engineered transaminase polypeptides described herein include, but are not limited to, compounds that are members of the vitamin B₆ family, selected from pyridoxal-5′-phosphate (also known as pyridoxal-phosphate, PLP, P5P), pyridoxine (PN), pyridoxal (PL), pyridoxamine (PM), and their phosphorylated counterparts; pyridoxine phosphate (PNP), and pyridoxamine phosphate (PMP). Accordingly, in some embodiments of the method, the suitable reaction conditions comprise the presence of a cofactor selected from PLP, pyridoxine (PN), pyridoxal (PL), pyridoxamine (PM), and their phosphorylated counterparts; pyridoxine phosphate (PNP), and pyridoxamine phosphate (PMP). In some embodiments, the cofactor is PLP. Suitable reaction conditions further can comprise the presence of a cofactor selected from PLP, PN, PL, PM, PNP, and PMP, at a concentration of about 0.1 mM to about 10 mM, 0.2 mM to about 5 mM, 0.5 mM to about 2.5 mM, about 10 mM or less, about 5 mM or less, about 2.5 mM or less, about 1.0 mM or less. In some embodiments, the suitable reaction conditions can further comprise the presence of the cofactor, PLP, at a concentration of about 0.1 g/L to about 10 g/L, 0.2 g/L to about 5 g/L, 0.5 g/L to about 2.5 g/L, about 10 g/L or less, about 5 g/L or less, about 2.5 g/L or less, about 1.0 g/L or less.

In some embodiments of the method (e.g., where whole cells or lysates are used), the cofactor is present naturally in the cell extract and does not need to be supplemented. In some embodiments of the method (e.g., using partially purified, or purified transaminase enzyme), the method can further comprise a step of adding cofactor to the enzyme reaction mixture. In some embodiments, the cofactor is added either at the beginning of the reaction and/or additional cofactor is added during the reaction.

In some embodiments of the method, the suitable reaction conditions can further comprise the presence of the reduced cofactor, nicotinamide adenine dinucleotide (NADH), which can act to limit the inactivation of the transaminase enzyme (see e.g., van Ophem et al., 1998, Biochemistry 37(9):2879-88). In such embodiments where NADH is present, a cofactor regeneration system, such as glucose dehydrogenase (GDH) and glucose or formate dehydrogenase and formate can be used to regenerate the NADH in the reaction medium.

Generally, the method of converting compound (1a) to compound (2a) using the engineering transaminase polypeptides of the present disclosure can be carried out wherein the suitable reaction conditions comprise a mixture of the substrate compound (1a) and its opposite enantiomer of compound (1b). Accordingly, in some embodiments, the suitable reaction conditions comprise that the mixture of compound (1a) and compound (1b) at the start of the reaction is a racemic mixture of compound (1).

As mentioned above, the substrate of compound (1a) and its opposite enantiomer of compound (1b) are capable of undergoing an epimerization reaction that provides an equilibrium between them (see Scheme 2 above) under certain conditions (e.g., preferably at least pH 9 and preferably at least 45° C.). Because the engineered transaminase polypeptides of the present disclosure exhibit a highly stereoselective preference for the substrate of compound (1a), this equilibrium between the two enantiomers provides for the ability to carry out a dynamic kinetic resolution (DKR) of the two enantiomers whereby the amount of product compound (2a) formed is greater than the starting amount of compound (1a). If the reaction occurs under conditions allowing the rapid conversion compound (1b) to compound (1a), the engineered polypeptide is able to convert more than the amount of compound (1a) present at the beginning of the reaction. Accordingly, in some embodiments of the method, the suitable reaction conditions comprise a mixture of an initial amount of the substrate compound (1a) with its opposite enantiomer of compound (1b) in a solution contacting the engineered polypeptide, wherein the solution is at least pH 9 and at least 45° C., wherein the amount of product compound (2a) formed by the conversion is greater than the initial amount of the substrate compound (1a) present in the solution. In some embodiments of the method, where the suitable reaction conditions comprise a racemic mixture of compound (1) (i.e., 50% of compound (1a) and 50% of compound (1b)), the yield of product of compound (2a) formed by the conversion reaction relative to the initial amount of the racemic compound (1) is greater than 50%, greater than 60%, greater than 70%, greater than 80%, greater than 90%, greater than 95%, or more. Because the DKR reaction is favored at conditions of at least pH 9 and 45° C., in some embodiments of the method, the suitable conditions can further comprise a solution pH of at least pH 9.5, at least pH 10.0, at least pH 10.5, at least pH 11.0, at least pH 11.5, and a solution temperature of at least 45° C., at least 50° C., at least 55° C., at least 60° C., or at least 65° C.

In some embodiments of the method, the suitable reaction conditions comprise a substrate compound (1a) loading of at least about 5 g/L, at least about 10 g/L, at least about 15 g/L, at least about 20 g/L, at least about 30 g/L, at least about 50 g/L, at least about 75 g/L, at least about 100 g/L, or even greater. In embodiments of the method wherein a racemic mixture of compound (1) is used, the suitable reaction conditions comprise a substrate of compound (1) loading of at least about 10 g/L, at least about 20 g/L, at least about 30 g/L, at least about 40 g/L, at least about 60 g/L, at least about 100 g/L, at least about 150 g/L, at least about 200 g/L, or even greater. The values for substrate loadings provided herein are based on the molecular weight of compound (1a), however it also contemplated that the equivalent molar amounts of various hydrates and salts of compound (1a) also can be used in the methods.

As noted above, in some embodiments the method is carried out in which the amino donor is IPM, and the suitable reaction conditions comprise an IPM concentration of at least about 0.5 M, at least about 1.0 M, at least about 2.5 M, at least about 5.0 M, at least about 7.5 M, at least about 10.0 M, or more. In some embodiments, when IPM is used as the amino donor, the method further comprises removal of the carbonyl by-product acetone which is formed from the isopropylamine.

In certain embodiments, the temperature of the suitable reaction conditions can be chosen to maximize the reaction rate at higher temperatures while maintaining the activity of the enzyme for sufficient duration for efficient conversion of the substrate to the product. Higher temperatures increase the rate of epimerization of compound (1b) to compound (1a), and thereby allow for a dynamic kinetic resolution process that provides increased product of compound (2a) yield from mixture of the substrate compound (1a) with it opposite enantiomer, compound (1b). Where higher temperatures are used, polypeptides with increased thermostability can be selected to carry out the process. The engineered polypeptides of the present disclosure have increased thermal stability relative to naturally occurring transaminase polypeptide e.g., the wild type polypeptide of SEQ ID NO: 2. This allows the engineered polypeptides to be used in methods for converting compound (1a) to compound (2a) at higher temperatures which can result in increased conversion rates and improved substrate solubility characteristics for the reaction, although substrate or product degradation at higher temperatures can contribute to decreased process yields. In some embodiments of the method the suitable reaction conditions comprise a temperature of between about 25° C. and about 75° C., between about 35° C. and about 65° C., between about 40° C. and about 60° C., at least about 30° C., at least about 35° C., at least about 40° C., at least about 45° C., or at least about 50° C., or about 60° C., or more. In certain embodiments, the temperature during the enzymatic reaction can be maintained at a temperature throughout the course of the reaction. In some embodiments, the temperature during the enzymatic reaction can be adjusted over a temperature profile during the course of the reaction.

The methods for preparing compound (2a) of the present disclosure are generally carried out in a solvent. Suitable solvents include water, aqueous buffer solutions, organic solvents, and/or co-solvent systems, which generally comprise aqueous solvents and organic solvents. The aqueous solvent (water or aqueous co-solvent system) may be pH-buffered or unbuffered.

In certain embodiments, the methods for preparing compound (2a) using the engineered transaminase polypeptides of the present disclosure can be carried out with the pH of the reaction mixture may be maintained at a desired pH or within a desired pH range by the addition of an acid or a base during the course of the reaction. In certain embodiments, the pH of the reaction mixture may be allowed to change, or be changed during the course of the reaction. Thus, it is contemplated that in some embodiments the pH may be controlled by using an aqueous solvent that comprises a buffer. Suitable buffers to maintain desired pH ranges are known in the art and include, for example, phosphate buffer, triethanolamine buffer, and the like. Combinations of buffering and acid or base addition may also be used. In some embodiments of the method the suitable reaction conditions comprise a solution pH of between about pH 8.5 and about pH 11.5, between about pH 9.0 and about pH 11.5, between about pH 9.5 and about pH 11.0, at least about pH 8.5, at least about pH 9.0, at least about pH 9.5, at least about pH 10.0, or at least about pH 10.5.

During the course of the transamination reactions, the pH of the reaction mixture may change. The pH of the reaction mixture may be maintained at a desired pH or within a desired pH range by the addition of an acid or a base during the course of the reaction. Alternatively, the pH may be controlled by using an aqueous solvent that comprises a buffer. Suitable buffers to maintain desired pH ranges are known in the art and include, for example, phosphate buffer, triethanolamine buffer, and the like. Combinations of buffering and acid or base addition may also be used. In some embodiments, the buffer is TEA (e.g., about 0.025 M to about 0.25 M TEA). In some embodiments of the method the suitable reaction conditions comprise a buffer solution of about 0.05 M borate to about 0.25 M borate, or about 0.1 M borate. In some embodiments, the reaction conditions comprise water as a suitable solvent with no buffer present.

In some embodiments, the methods for preparing compound (1a) using an engineered transaminase polypeptide described are generally carried out in an aqueous co-solvent system comprising an organic solvent (e.g., ethanol, isopropanol (IPA), dimethyl sulfoxide (DMSO), ethyl acetate, butyl acetate, 1-octanol, heptane, octane, methyl t-butyl ether (MTBE), toluene, and the like), ionic liquids (e.g., 1-ethyl 4-methylimidazolium tetrafluoroborate, 1-butyl-3-methylimidazolium tetrafluoroborate, 1-butyl-3-methylimidazolium hexafluorophosphate, and the like). The organic solvent component of an aqueous co-solvent system may be miscible with the aqueous component, providing a single liquid phase, or may be partly miscible or immiscible with the aqueous component, providing two liquid phases. Exemplary aqueous co-solvent systems comprises water and one or more organic solvent. In general, an organic solvent component of an aqueous co-solvent system is selected such that it does not completely inactivate the transaminase enzyme. Appropriate co-solvent systems can be readily identified by measuring the enzymatic activity of the specified engineered transaminase enzyme with a defined substrate of interest in the candidate solvent system, utilizing an enzyme activity assay, such as those described herein. In some embodiments of the method, the suitable reaction conditions comprise an aqueous co-solvent comprising DMSO at a concentration of at least about 5% (v/v), at least about 10% (v/v), at least about 20% (v/v), at least about 30% (v/v), or at least about 40% (v/v).

The suitable reaction conditions used in the method can comprise a combination of reaction parameters that provide for the biocatalytic conversion of compound (1a) to compound (2a) in a higher diastereomeric ratio relative to compound (2c) and in a higher percentage conversion. Accordingly, in some embodiments of the method, the combination of reaction parameters comprises: (a) substrate loading of about 10-100 g/L compound (1a); (b) polypeptide concentration of about 1.0-40 g/L; (c) IPM concentration of about 0.1-10 M; (d) PLP cofactor at a concentration of about 0.1-1.0 g/L; (e) about pH 8.5-11.0; and (f) temperature of about 30-60° C. In some embodiments, the combination of reaction parameters comprises: (a) at least about 40 g/L compound (1a); (b) about 10 g/L or less of engineered polypeptide; (c) at least about 1 M isopropylamine; (d) about 1 g/L PLP; (e) about 0.2 M borate; (f) about 20% (v/v) DMSO; (g) about pH 10.5; and (h) a temperature of about 45° C. Further exemplary reaction conditions include the assay conditions provided in Tables 2A, 2B, 2C, and 2D and Example 1. Exemplary reaction conditions for a process of making compound (2a) on a 40 g scale also include the conditions provided in Example 2.

The engineered polypeptides of the present disclosure have improved properties in the biocatalytic conversion of compound (1a) to compound (2a) and can provide increased yields of the product in higher diastereomeric ratio in a shorter time periods with a smaller amount of enzyme than the wild type polypeptide of SEQ ID NO: 2 or the engineered polypeptides SEQ ID NO: 4 or 6. Accordingly, in some embodiments of the method, the suitable reaction conditions comprise a substrate loading of compound (1a) of at least about 20 g/L, 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, or more, and wherein the method results in at least about 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or greater conversion of compound (1a) to compound (2a) in about 48 h or less, in about 36 h or less, or in about 24 h or less.

In some embodiments of the method, the suitable reaction conditions comprise a substrate loading of compound (1a) of at least about 20 g/L, 30 g/L, 40 g/L, 50 g/L, 60 g/L, 70 g/L, 100 g/L, or more, and the method results in the conversion of the racemic mixture of compound (1) to the product compound (2a) in a diastereomeric ratio relative to compound (2c) of at least about 2:1, at least about 3:1, at least about 4:1, at least about 8:1, at least about 10:1, at least about 15:1, at least about 20:1, or at least about 30:1, in about 48 h or less, in about 36 h or less, or in about 24 h or less. Further, in embodiments where the suitable reaction conditions suitable that allow for the epimerization of compound (1b) to compound (1a), the method can provide a dynamic kinetic resolution and the yield of product of compound (2a) formed by the reaction relative to the starting amount of the compound (1) is greater than 50%, greater than 60%, greater than 70%, greater than 80%, greater than 90%, greater than 95%, or more.

In carrying out the transamination reactions described herein, the engineered transaminase polypeptide may be added to the reaction mixture in the form of a purified enzyme, whole cells transformed with gene(s) encoding the enzyme, and/or as cell extracts and/or lysates of such cells. Whole cells transformed with gene(s) encoding the engineered transaminase enzyme or cell extracts, lysates thereof, and isolated enzymes may be employed in a variety of different forms, including solid (e.g., lyophilized, spray-dried, and the like) or semisolid (e.g., a crude paste). The cell extracts or cell lysates may be partially purified by precipitation (ammonium sulfate, polyethyleneimine, heat treatment or the like, followed by a desalting procedure prior to lyophilization (e.g., ultrafiltration, dialysis, and the like). Any of the cell preparations may be stabilized by crosslinking using known crosslinking agents, such as, for example, glutaraldehyde or immobilization to a solid phase (e.g., Eupergit C, and the like). In some embodiments where the engineered polypeptide can be expressed in the form of a secreted polypeptide and the culture medium containing the secreted polypeptides can be used in the method of converting compound (1a) to compound (2a).

In some embodiments, solid reactants (e.g., enzyme, salts, etc.) may be provided to the reaction in a variety of different forms, including powder (e.g., lyophilized, spray dried, and the like), solution, emulsion, suspension, and the like. The reactants can be readily lyophilized or spray dried using methods and equipment that are known to those having ordinary skill in the art. For example, the protein solution can be frozen at −80° C. in small aliquots, then added to a pre-chilled lyophilization chamber, followed by the application of a vacuum.

In some embodiments, the order of addition of reactants is not critical. The reactants may be added together at the same time to a solvent (e.g., monophasic solvent, biphasic aqueous co-solvent system, and the like), or alternatively, some of the reactants may be added separately, and some together at different time points. For example, the cofactor, transaminase, and transaminase substrate may be added first to the solvent. For improved mixing efficiency when an aqueous co-solvent system is used, the transaminase, and cofactor may be added and mixed into the aqueous phase first. The organic phase may then be added and mixed in, followed by addition of the transaminase substrate. Alternatively, the transaminase substrate may be premixed in the organic phase, prior to addition to the aqueous phase.

The quantities of reactants used in the transamination reaction will generally vary depending on the quantities of product desired, and concomitantly the amount of transaminase substrate employed. Those having ordinary skill in the art will readily understand how to vary these quantities to tailor them to the desired level of productivity and scale of production. In general, the transaminase substrates are kept at levels that achieve essentially complete or near complete conversion of the substrates into products. Generally, the transamination reaction is generally allowed to proceed until essentially complete, or near complete, transformation of substrate is obtained. Transformation of substrate to product can be monitored using known methods by detecting substrate and/or product. Suitable methods include gas chromatography, HPLC, and the like.

In some embodiments, the method can further comprise a step of removal of the carbonyl by-product formed from the amino group donor when the amino group is transferred to the substrate of compound (1a). Such removal in situ can reduce the rate of the reverse reaction such that the forward reaction dominates and more substrate is then converted to product. Removal of the carbonyl by-product can be carried in a number of ways. Where the amino group donor is an amino acid, such as alanine, the carbonyl by product, a keto acid, can be removed by reaction with a peroxide (see, e.g., US 2008/0213845, incorporated herein by reference). Peroxides which can be used include, among others, hydrogen peroxide; peroxyacids (peracids) such as peracetic acid (CH₃CO₃H), trifluoroperacetic acid and metachloroperoxybenzoic acid; organic peroxides such as t-butyl peroxide ((CH₃)₃COOH), or other selective oxidants such as tetrapropylammonium perruthenate, MnO₂, KMnO₄, ruthenium tetroxide and related compounds. Alternatively, pyruvate removal can be achieved via its reduction to lactate by employing lactate dehydrogenase to shift equilibrium to the product amine (see, e.g., Koszelewski et al., 2008, Adv. Syn. Catal. 350: 2761-2766). Pyruvate removal can also be achieved via its decarboxylation to carbon dioxide acetaldehyde by employing pyruvate decarboxylase (see, e.g., Höhne et al., 2008, Chem BioChem 9: 363-365).

In some embodiments, where the choice of the amino donor results in a carbonyl by-product that has a vapor pressure higher than water (e.g., a low boiling co-product such as a volatile organic carbonyl compound), the carbonyl by-product can be removed by sparging the reaction solution with a non-reactive gas or by applying a vacuum to lower the reaction pressure and removing the carbonyl by-product present in the gas phase. A non-reactive gas is any gas that does not react with the reaction components. Various non-reactive gases include nitrogen and noble gases (e.g., inert gases). In some embodiments, the non-reactive gas is nitrogen gas.

In some embodiments, the amino donor used in the process is isopropylamine (IPM), which forms the carbonyl by-product acetone upon transfer of the amino group to the amino group acceptor. The acetone can be removed by sparging with nitrogen gas or applying a vacuum to the reaction solution and removing the acetone from the gas phase by an acetone trap, such as a condenser or other cold trap. Alternatively, the acetone can be removed by reduction to isopropanol using a ketoreductase.

In some embodiments of the process where the carbonyl by-product is removed, the corresponding amino group donor can be added during the transamination reaction to replenish the amino group donor and/or maintain the pH of the reaction. Replenishing the amino group donor also shifts the equilibrium towards product formation, thereby increasing the conversion of substrate to product. Thus, in some embodiments wherein the amino group donor is IPM and the acetone product is removed in situ, the method can further comprise a step of adding IPM to the reaction solution to replenish the amino group donor lost during the acetone removal and to maintain the pH of the reaction (e.g., at about 8.5).

Alternatively, in embodiments where an amino acid is used as amino group donor, the keto acid carbonyl by-product can be recycled back to the amino acid by reaction with ammonia and NADH using an appropriate amino acid dehydrogenase enzyme, thereby replenishing the amino group donor.

In some embodiments, the present disclosure also contemplates that the method comprising the biocatalytic conversion compound (1a) to compound (2a) using an engineered transaminase polypeptide can further comprise chemical steps of compound (2a) product work-up, extraction, isolation, purification, and/or crystallization, each of which can be carried out under a range of conditions.

In some embodiments, the present disclosure also contemplates that the method comprising the biocatalytic conversion compound (1a) to compound (2a) using an engineered transaminase polypeptide of the present disclosure can further comprise one or more further chemical steps for converting compound (2a) to the pharmaceutical ingredient of compound (3) (IUPAC name: (3R)-1-[(1R,2R)-2-[2-(3,4-dimethoxyphenyl)ethoxy]cyclohexyl]pyrrolidin-3-ol), or its salts, hydrates, or solvates. Processes for the synthesis of compound (3) that include a non-biocatalytic chemical step of converting compound (1a) to compound (2a) are already known in the art (see e.g., PCT Publ. No. WO2006/138673A2). Thus, any of the above described biocatalytic methods for converting compound (1a) (or the racemic mixture of compound (1)) to compound (2a) can immediately be incorporated as a step into such known processes for making compound (3). Accordingly, in some embodiments the present disclosure provides a process for preparing compound (3) wherein the process comprises the steps of: (a) preparing compound (2a) according to any of the above disclosed methods for the biocatalytic conversion of compound (1a) to compound (2a) in at least a 2:1 diastereomeric ratio relative to compound (2c) under suitable reaction conditions; and (b) preparing compound (3) from compound (2a). In some embodiments, the method for preparing compound (3) comprises: (a) contacting compound (1a) with an engineered transaminase polypeptide disclosed herein in the presence of an amino donor under suitable reaction conditions, thereby preparing compound (2a); and (b) prepare compound (3) from compound (2a). The engineered transaminase polypeptides disclosed herein useful in the process for preparing compound (3) include e.g., any of the above described engineered transaminase polypeptides having one or more amino acid residue differences as compared to SEQ ID NO: 6, and capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, including the exemplary polypeptides of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, and the variants of those sequences disclosed herein. Such variants, include but are not limited to, engineered transaminase polypeptides comprising an amino acid sequence having at least 80% sequence identity to the reference polypeptide of SEQ ID NO: 6 and an amino acid residue difference as compared to SEQ ID NO: 6 at one or more of the following positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. In some embodiments, the amino acid residue differences as compared to SEQ ID NO: 6 are selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X69C; X69V; X69W; X94L; X99L; X108V; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X135Q; X136W; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I.

Also, in some embodiments the present disclosure provides a process for the preparation of the compound (3), wherein a step in the process comprises contacting (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone (compound (1a)) or an analog of compound (1a) with an engineered transaminase polypeptide disclosed herein in the presence of an amino donor under reaction conditions suitable for conversion of compound (1a) or an analog of compound (1a) to (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound (2a)) or an analog of compound (2a) in enantiomeric and diastereomeric excess. Any of the methods and/or reaction conditions disclosed herein for converting compound (1a) or an analog of compound (1a) to compound (2a) or an analog of compound (2a) using the engineered transaminases of the disclosure can be used in the step of the process. Additionally, any of the engineered transaminase polypeptides disclosed herein can be used in the step in the process for preparing compound (3) including e.g., any of the above described engineered transaminase polypeptides having one or more amino acid residue differences as compared to SEQ ID NO: 6, and capable of converting a racemic mixture of compound (1) to the (1R,2R)-trans amine product of compound (2a) in at least a 2:1 diastereomeric ratio relative to the (1R,2S)-cis amine product of compound (2c) under suitable reaction conditions, including the exemplary polypeptides of SEQ ID NO: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, and the variants of those sequences disclosed herein. Such variants, include but are not limited to, engineered transaminase polypeptides comprising an amino acid sequence having at least 80% sequence identity to the reference polypeptide of SEQ ID NO: 6 and an amino acid residue difference as compared to SEQ ID NO: 6 at one or more of the following positions: X2; X4; X5; X7; X8; X9; X10; X11; X14; X22; X28; X37; X38; X41; X42; X44; X52; X54; X55; X56; X58; X69; X94; X99; X108; X124; X126; X135; X136; X141; X142; X150; X155; X156; X157; X164; X165; X171; X182; X199; X209; X210; X213; X215; X217; X218; X223; X245; X257; X265; X267; X296; and X328. In some embodiments, the amino acid residue differences as compared to SEQ ID NO: 6 are selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X22I; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X69C; X69V; X69W; X94L; X99L; X108V; X124F; X124I; X124L; X124R; X124V; X126A; X126T; X135Q; X136W; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I.

In some embodiments any of the above described methods for the conversion of compound (1a) to compound (2a) can be carried out wherein the method comprises contacting an analog of compound (1a) with an engineered transaminase polypeptide of the present disclosure (e.g., as described in Tables 2A, 2B, 2C, and 2D and elsewhere herein) in the presence of an amino donor under suitable reaction conditions, thereby resulting in the preparation of the chiral amine of the corresponding analog of product compound (2a) in diastereomeric excess. Suitable reactions conditions for the conversion of analogs of compound (1a) to the chiral amine of the corresponding analogs of compound (2a) can be the same as used for compound (1a) or determined by the ordinary artisan based on the known properties of the analog compounds and routine experimentation.

Accordingly, in some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein the analog of compound (1a) is a compound of Formula I. Accordingly, in some embodiments a method for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein the analog of compound (1a) is a compound of Formula I

wherein, Ar is an optionally substituted aromatic ring selected from phenyl, fused phenyl, heteroaryl, or fused heteroaryl; X is selected from N, O, CH₂, and S; m=1 to 6; n=1 to 6; and the analog of compound (2a) prepared is a compound of Formula II

In some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein Ar is phenyl, optionally substituted with one or two substituents selected from halogen or OR, where R is H, alkyl or aryl ether, alkyl or aryl ester, carbonate, sulfonate, or phosphate.

In some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein Ar is selected from 3,4-dimethoxyphenyl, 3,4-dihydroxyphenyl, or 3,4-dihalophenyl.

In some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein X is O; m=1 or 2; and n=2 or 3.

In some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein Ar is phenyl, optionally substituted with one or two substituents selected from halogen or OR, where R is H, alkyl or aryl ether, alkyl or aryl ester, carbonate, sulfonate, or phosphate; X is O; m=1 or 2; and n=2 or 3.

In some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein Ar is selected from 3,4-dimethoxyphenyl, 3,4-dihydroxyphenyl, or 3,4-dihalophenyl; X is N, O, or S; m=1 or 2; and n=2 or 3. In some embodiments, one or more of the hydroxy groups on the aryl group are protected with a hydroxyl protecting group selected from the group consisting of acetyl, benzyl, benzoyl, methyl, methoxy, tert-butyloxycarbonyl, para-methoxybenzyl, benzylidine, dimethylacetal, silyl, tert-butyl-diphenylsilyl, and trimethylsilyl. Other examples of hydroxyl protecting groups that may be the R group of compounds of Formula II undergoing the biocatalytic methods of the present disclosure can be found in P. G. M. Wuts and T. W. Greene, “Greene's Protective Groups in Organic Synthesis—Fourth Edition,” John Wiley and Sons, New York, N.Y., 2007, Chapter 7 (“Greene”).

In some embodiments, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out wherein the analog of compound (1a) is a deuterated version of the compound (1a) (i.e., a molecule have the same structure as compound (1a) but with one or more the hydrogen atoms of compound (1a) substituted with a deuterium atom) (see e.g., U.S. Pat. No. 7,705,036 B2). Similarly, the methods for the conversion of an analog of compound (1a) to an analog of compound (2a) can be carried out with the deuterated version of any of the above described analog compounds of Formula I.

In further embodiments, any of the above described methods for the conversion of compound (1a) (or an analog of compound (1a)) to compound (2a) (or an analog of compound (2a)) can be carried out wherein the method further comprises one or more steps selected from: extraction of compound (2a) or the analog of compound (2a); isolation of compound (2a) or the analog of compound (2a); forming a salt of compound (2a) or the analog of compound (2a); purification of compound (2a) or the analog of compound (2a); and crystallization of compound (2a) or the analog of compound (2a).

In some embodiments, a salt of compound (2a) is formed by addition of an inorganic or protic organic acid to a mixture comprising compound (2a), wherein the inorganic or protic organic acid is selected from HCl, H₂SO₄, oxalic, pivalic, L- or D-malic, or maleic acid. Accordingly, in some embodiments, the above described methods can be carried out wherein the methods comprise a further step of forming a chloride, sulfate, oxalate, pivalate, malate, or maleate salt of compound (2a). In one embodiment, the salt formed is a maleate salt of compound (2a). In one embodiment, the salt formed is a D-malate salt of compound (2a).

Methods, techniques, and protocols for extracting, isolating, forming a salt of, purifying, and/or crystallizing compound (2a) or its analogs from biocatalytic reaction mixtures produced by the above disclosed methods are known to the ordinary artisan and/or accessed through routine experimentation. Additionally, illustrative methods are provided in the Examples below.

Various features and embodiments of the disclosure are illustrated in the following representative examples, which are intended to be illustrative, and not limiting.

6. EXAMPLES Example 1 Synthesis, Optimization, and Screening of Engineered Transaminase Polypeptides

Gene Synthesis and Optimization:

The polynucleotide sequence encoding the reported wild-type omega transaminase polypeptide from Arthrobacter sp. KNK168 of SEQ ID NO: 2 with a single amino acid change (I306V) was codon optimized and synthesized as the gene of SEQ ID NO: 3. The synthetic gene of SEQ ID NO: 3 was cloned into a pCK110900 vector system (see e.g., US Patent Application Publication 20060195947, which is hereby incorporated by reference herein) and subsequently expressed in E. coli W3110fhuA. The E. coli W3110 expresses the transaminase polypeptides as an intracellular protein under the control of the lac promoter. The polypeptide accumulates primarily as a soluble cytosolic active enzyme. HTP assays used for primary screening were carried out using the cleared cell-lysate from expression of these E. coli W3110 cells (see below). The synthetic gene of SEQ ID NO: 3 was optimized for increased expression and thermostability by inserting active and silent mutations which are described in U.S. application Ser. No. 12/714,397, filed Feb. 26, 2010, which is incorporated herein by reference. This optimization resulted in the synthetic gene of SEQ ID NO: 5 encoding the engineered polypeptide of SEQ ID NO: 6, which has the following 24 amino acid differences relative to the naturally occurring transaminase of Arthrobacter sp. KNK168 (SEQ ID NO: 2): S8P; Y60F; L61Y; H62T; V65A; V69T; D81G; M94I; 196L; F1221; G136F; A169L; V1991; A209L; G215C; G217N; S223P; L269P; L273Y; T282S; A284G; P297S; I306V; and S321P.

The engineered polypeptide of SEQ ID NO: 6 was used as the starting backbone for further optimization to generate genes encoding the engineered transaminase polypeptides of SEQ ID NOs: 8, 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150, 152, 154, 156, 158, 160, 162, 164, 166, 168, 170, 172, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192, 194, 196, 198, 200, 202, 204, and 206, each of which is capable of converting compound (1a) to compound (2a) with improved enzyme properties relative to it and/or the reference polypeptides SEQ ID NOs: 6. Further optimization of the gene of SEQ ID NO: 5 was carried out using the standard methods of directed evolution via iterative variant library generation by gene synthesis followed by screening and sequencing of hits.

Production of Shake Flask Powders (SFP):

A shake-flask procedure was used to generate engineered transaminase polypeptide powders used in secondary screening assays or in the biocatalytic methods of converting compound (1a) to compound (2a) disclosed herein. Shake flask powder (SFP) include approximately 30% total protein and accordingly provide a more purified preparation of an engineered enzyme as compared to the cell lysate used in HTP assays. A single microbial colony of E. coli containing a plasmid encoding an engineered transaminase of interest is inoculated into 50 mL Luria Bertani broth containing 30 mg/ml chloramphenicol and 1% glucose. Cells are grown overnight (at least 16 hours) in an incubator at 30° C. with shaking at 250 rpm. The culture is diluted into 250 mL Terrific Broth (12 g/L bacto-tryptone, 24 g/L yeast extract, 4 mL/L glycerol, 65 mM potassium phosphate, pH 7.0, 1 mM MgSO₄) containing 30 μg/ml chloramphenicol, in a 1 liter flask to an optical density at 600 nm (OD600) of 0.2 and allowed to grow at 30° C. Expression of the transaminase gene is induced by addition of isopropyl-β-D-thiogalactoside (“IPTG”) to a final concentration of 1 mM when the OD600 of the culture is 0.6 to 0.8 and incubation is then continued overnight (at least 16 hours). Cells are harvested by centrifugation (5000 rpm, 15 min, 4° C.) and the supernatant discarded. The cell pellet is resuspended with an equal volume of cold (4° C.) 100 mM triethanolamine (chloride) buffer, pH 7.0 (optionally including 2 mM MgSO₄), and harvested by centrifugation as above. The washed cells are resuspended in two volumes of the cold triethanolamine (chloride) buffer and passed through a French Press twice at 12,000 psi while maintained at 4° C. Cell debris is removed by centrifugation (9000 rpm, 45 minutes, 4° C.). The clear lysate supernatant was collected and stored at −20° C. Lyophilization of frozen clear lysate provides a dry shake-flask powder of crude transaminase polypeptide. Alternatively, the cell pellet (before or after washing) can be stored at 4° C. or −80° C.

HTP Assay:

Primary screening used to guide optimization was carried out in a ˜200 μL volume in 96-well plate high-throughput (HTP) assay protocol using cell lysates. For the HTP assay data provided in Table 2B, the general HTP assay conditions were: 50 g/L substrate mixture of compound (1), 40 μL of clear cell lysate containing the engineered transaminase polypeptide, 1 g/L PLP, 1 M IPM, in an aqueous co-solvent solution of 0.2 M borate buffer, 40% (v/v) DMSO, pH 10.5, 45° C. reaction temperature and 4 h reaction time (with 200 rpm shaking). The details of the HTP assay protocol are as follows. The stock assay solution was prepared by mixing the following: 4.00 mL of 5 M isopropylamine (IPM) in 0.2 M boric acid; 2.00 mL of 10 g/L PLP in sterile water; 7.00 mL of DMSO; and 2.00 mL of 0.2 M boric acid. This stock assay solution was adjusted to pH 10.5 (with concentrated HCl or 10 M NaOH) upon stirring and 150 μL/well of the solution were dispensed into a 96 deep well plate. The plate was heat sealed and incubated at 45° C. while shaking (200 rpm) for at least 15 minutes. Clear cell lysate containing the engineered polypeptide variant to be screened was prepared by shaking cells in 0.5 mg/mL Lysozyme, 0.4 mg/mL PMBS, 0.2 M borate, pH 10.5, for 1 h at room temperature, followed by centrifugation at 5000 rpm and 4° C. for 10 min. A 40 μL volume of the clear cell lysate (taken from a total 300 μL/well volume of lysate) was then added to each well containing the 150 μL of the stock assay solution. A substrate stock solution was prepared in DMSO as follows: 28.7 g/L of 87 wt % racemic substrate mixture of compound (1) dissolved in 25 mL DMSO along with 2.5 g of biphenyl to provide a final solution volume of 52 mL. The HTP assay reaction was then initiated by the addition of 21 μL/well of the substrate stock solution to the plate, which then was heat sealed and shaken (200 rpm) at 45° C. for 4 h. After 4 h, the reaction was quenched by addition of 800 μL/well of MeOH followed by heat sealing and a quick further shaking to ensure homogeneity. After centrifugation, a 20 μL/well sample was diluted into 180 μL/well of MeOH for achiral HPLC analysis as described below.

For the HTP assay data provided in Table 2A, the HTP assays were carried out as above but with the following slightly modified general reaction conditions: 5 g/L of a racemic substrate mixture of compound (1), 100 μL clear cell lysate containing the engineered transaminase polypeptide, 1 M isopropylamine (IPM), 1 mM PLP, 100 mM TEA, pH 10.0, 45° C. and 2 h reaction time with 245 rpm shaking. Cells were lysed by shaking for 0.5 to 1 hour at 250 rpm and 37° C. in 1 mL of lysis buffer containing 100 mM triethanolamine, 0.5 g/L lysozyme, and 0.4 g/L polymyxin B sulfate at pH 9.0. Rather than quenching with MeOH, a 50 μL aliquot was removed and added to 100 μL acetonitrile, and 10 μL of this is injected onto an achiral HPLC column for analysis as described below.

SFP Assay:

In addition to the HTP assay for primary screening, in some cases a secondary screening was carried out on a 2.00 mL scale using shake-flask powder (SFP) preparations of the engineered transaminase polypeptides. The general SFP assay reaction conditions (specific conditions are noted in Tables 2A, 2B, 2C, and 2D), were as follows: 10 g/L or 100 g/L substrate mixture of compound (1), 1.0 g/L of the engineered transaminase polypeptide SFP, 1.0 g/L PLP, 1 M IPM, in an aqueous co-solvent solution of 0.2 M borate buffer or 0.1M TEA buffer, 20% or 40% (v/v) DMSO (as noted in Tables 2A, 2B, 2C, and 2D), pH 10.0 or pH 10.5, 45° C. reaction temperature and 4.5 h, 15-18 h, or 24 h reaction time (with 400 rpm shaking). The details of the SFP assay protocol are as follows. The stock assay solution was prepared as follows: to 4.00 mL of 5M IPM in 0.2 M boric acid (pH not adjusted) was added 2.00 mL of 10 g/L PLP in sterile water followed by 6.00 mL of DMSO and 4.00 mL of 0.2 M boric acid (pH not adjusted). The stock assay solution was then adjusted to pH 10.5 using concentrated HCl. For each experiment 1.60 mL of stock assay solution was added into a screw cap vial, which was then tightly closed and heated to 45° C. with magnetic stirring (400 rpm). Stock enzyme solution was prepared by dissolving 20 mg of engineered polypeptide SFP in 2.00 mL of 0.2 M borate, pH 10.5 buffer (0.2 M boric acid solution adjusted to pH 10.5 using 10M NaOH). After 15 min, 200 μL of a 10.0 g/L enzyme stock solution was added to the reaction mixture at 45° C. Immediately after addition of the enzyme stock solution, 420 μL of a substrate stock solution was then added to start the reaction (substrate stock solution: 28.7 g/L of 87 wt % racemic substrate mixture of compound (1) in 25 mL DMSO with 2.5 g of biphenyl to provide a final volume of 52 mL). The vial was tightly closed and the reaction was left to proceed upon stirring (400 rpm) at 45° C. for 48 h with the 24 h time point used for comparison of SFP assay results. The course of the SFP assay reaction was monitored over the 48 h time course by taking 5 μL samples, diluting in 1.00 mL of MeOH, and then directly injecting into the HPLC for analysis.

HPLC Analysis of Assay Samples:

After running the HTP or SFP assays, as described above, samples from the quenched assay reaction solutions were analyzed using achiral HPLC to determine the conversion of the racemic mixture of compound (1) to the product of compound (2a), and/or to determine the diastereomeric ratio of the products. Additionally, SFP assay samples were analyzed using chiral HPLC to confirm that the engineered polypeptides were producing >99% e.e. of the R-amine products (i.e., compound (2a) and compound (2c)) relative to the S-amine products.

Analysis of the HTP and SFP assay reaction samples to provide results for trans:cis ratio, % d.e., relative activity, and % conversion as summarized in Table 2A were carried using achiral HPLC on either a Phenomenex Luna C18 or an Ascentis C18 column. Samples were prepared as follows: after reaction remove 50 μL aliquot and add to 100 μL of acetonitrile in a shallow well plate; centrifuge plate at 4000 rpm for 10 min; inject 10 μL into HPLC. The HPLC conditions and instrumental parameters are shown below in Tables 3 and 4.

TABLE 3 Achiral HPLC on Phenomenex Luna C18 column Column: Phenomenex Luna C18(2), 10 cm × 4.6 mm, 5 μm, cat 00D-4252-E0 Flow rate: 2.0 mL/min Column temp: 40° C. Solvents A: 0.1% TFA in DI water; B: neat MeCN Solvent program: Step Time Module Action Value 1 0.01 Pumps Pump B Conc. 25.0 2 1.10 Pumps Pump B Conc. 25.0 3 1.35 Pumps Pump B Conc. 100.0 4 2.25 Pumps Pump B Conc. 100.0 5 2.26 Pumps Pump B Conc. 25.0 6 2.70 Controller Stop Total program time: 2.7 min Detector wavelength: 275 nm Retention times: trans isomer = 1.8 min; cis isomer = 2.2 min; ketone substrate = 2.4 min

TABLE 4 Achiral HPLC on Ascentis Express C18 column Column: Ascentis Express C18, 15 cm × 4.6 mm, 2.7 μm, cat 53829-U Flow rate: 1.0 mL/min Column temp: 40° C. Solvents A: 20 mM NH₄OAc in DI water; B: neat MeCN Solvent program: Step Time Module Action Value 1 0.01 Pumps Pump B Conc. 30.0 2 1.00 Pumps Pump B Conc. 30.0 3 2.50 Pumps Pump B Conc. 100.0 4 3.00 Pumps Pump B Conc. 100.0 5 3.01 Pumps Pump B Conc. 30.0 6 4.75 Controller Stop Total program time: 4.75 min Detector wavelength: 275 nm Retention times: trans isomer = 3.2 min; cis isomer = 3.3 min; ketone substrate = 4.3 min

Analysis of SFP assay reaction samples to provide results for trans:cis ratio as summarized in Table 2B were carried out using achiral HPLC on a Zorbax SB-C18 column according to the conditions and instrumental parameters shown in Table 5.

TABLE 5 Achiral HPLC on Zorbax SB-C18 for HTP Assay Column: Zorbax SB-C18 (75 × 4.6 mm, 3.5 um) Flow rate: 1.5 mL/min Column temp: 30° C. Solvents A: 85% MeOH, 15% DI Water, 0.05% Diethylamine Solvent program: isocratic Total program time: 1.40 min Detector wavelength: 280 nm Retention times: ketone substrate = 0.7 min; trans isomer = 0.8 min; cis isomer = 1.0 min

Analysis of HTP assay reaction samples to provide results for percent conversion used to determine relative activity as summarized in Table 2B were carried out using achiral HPLC on an Ascentis Express C18 column according to the conditions and instrumental parameters shown in Table 6.

TABLE 6 Achiral HPLC on Ascentis Express C18 column for SFP testing Column: Ascentis express C18 (100 × 4.6, 2.7 um) Flow rate: see program Column temp: 25° C. Solvents A: 0.05% H₃PO₄ (pH = 2.25) in DI water; B: neat MeCN Program: Step Time Module Action Value Action Value 1 0.01 Pumps Pump B Conc. 25.0 Flow rate 1.6 mL/min 2 2.00 Pumps Pump B Conc. 36.0 Flow rate 1.6 mL/min 3 2.05 Pumps Pump B Conc. 50.0 Flow rate 2.0 mL/min 4 4.00 Pumps Pump B Conc. 50.0 Flow rate 2.0 mL/min 5 4.05 Pumps Pump B Conc. 100.0 Flow rate 2.0 mL/min 6 5.50 Pumps Pump B Conc. 100.0 Flow rate 2.0 mL/min 7 5.51 Pumps Pump B Conc. 25.0 Flow rate 1.6 mL/min 8 6.5 Controller Stop Total program time: 6.5 min Detector wavelength: 280 nm Retention times: trans isomer = 1.2 min; cis isomer = 1.4 min; ketone substrate = 3.6 min

Additionally, as noted in Table 2A, the production of the R-amine products relative to S-amine products in enantiomeric excess of 99% e.e. was confirmed using chiral HPLC analysis of polypeptide SFP assay samples from the following engineered polypeptides: SEQ ID NO: 6, 8, 12, 16, 18, 40, 42, 44, 46, 48, 50, 52, 58, 66, and 82. Chiral HPLC was carried out according to the following sample derivatization protocol and using a Diacel Chiralcel OJ-RH column according to the conditions and instrumental parameters shown in Table 7.

Derivatization:

SFP assay samples were transferred to vials. Saturated potassium carbonate (200 μL) was added followed by ethyl acetate (1 mL). The vials were vortexed, and the phases were allowed to separate. The organic layer (700 μL) was transferred to a fresh vial and evaporated under nitrogen purge (removes any extracted isopropylamine). To each vial was added 100 mL of derivatizing solution (5 mL ethyl acetate+250 μL triethylamine+125 μL acetic anhydride). After 5 to 10 min of reaction, the solution was evaporated under nitrogen purge, and 200 μL acetonitrile was added to resuspend the sample.

TABLE 7 Chiral HPLC on Diacel Chiralcel OJ-RH column Column: Diacel Chiralcel OJ-RH, 150 mm × 4.6 mm, 5 μm Temp: 40° C. Flow rate: 1.5 ml/min Solvents: A: 0.1% H₃PO₄ in DI water B: neat MeCN Solvent program Step Time Module Action Value 1 0.01 Pumps Pump B Conc. 20.0 2 10.00 Pumps Pump B Conc. 20.0 3 12.00 Pumps Pump B Conc. 70.0 4 14.00 Pumps Pump B Conc. 70.0 5 16.00 Pumps Pump B Conc. 20.0 6 20.00 Controller Stop Total program time: 20 min Detector wavelength: 275 nm Retention times: (R)-trans isomer = 6.0 min; (S)-trans isomer = 6.5 min; (R)-cis isomer = 12.4 min; (S)-cis isomer = 13.4 min.

Example 2 Biocatalytic Production of (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound 2(a)) at 40 g Scale

The following example illustrates a method for preparing the compound (3) precursor of compound (2a) in a biocatalytic reaction using an engineered polypeptide of the present disclosure.

A 2000 mL RB flask was charged with 8 g of the engineered transaminase polypeptide of SEQ ID NO: 18 and 800 mg of PLP. A 640 mL solution of 1M isopropyl amine (IPM) in 0.2 M borate buffer at pH 10.5 was added to the RB flask. The slurry was stirred at ambient temperature (20-25° C.) with a magnetic stir bar to allow as much transaminase polypeptide to dissolve as possible. DMSO (80 mL) was added and the resulting slurry was heated to 45° C. Once at 45° C., the pH of the slurry was adjusted to exactly pH 10.5 using 4 M IPM and a free standing titrating unit.

A racemic mixture of compound (1) (40.0 g, 142 mmol), comprising the substrate of compound (1a) and its opposite enantiomer of compound (1b), was dissolved in DMSO (80 mL). This substrate solution then was added to the heated transaminase polypeptide slurry at a controlled rate over 30 minutes. The resulting reaction mixture was a milky yellow slurry.

The reaction mixture was aged 16 hours with the pH controlled at pH 10.5 by addition of IPM. At 16 hours, the slurry was sampled and 90% conversion was observed by HPLC. The reaction mixture was aged another 5 hours at 45° C. without pH control. The reaction mixture was sampled again at 21 hours and >94% conversion was observed by HPLC.

The reaction mixture was then allowed to cool to ambient temperature, after which the slurry was extracted three times with 1:1 isopropanol:tert-butyl methyl ether (800 mL/20 vol for each extraction). The lower aqueous phase was discarded. The combined organic extracts were concentrated to a low volume at 30-40° C./5-25 mm Hg. The resulting mixture was diluted with tert-butyl methyl ether (400 mL) then washed with 1 M potassium carbonate that had been saturated with potassium chloride (400 mL). The lower aqueous phase was discarded.

The upper organic layer was solvent switched to 2-butanol. The resulting solution was filtered through celite, then diluted with 2-butanol to a total volume of 125 mL and cooled below 5° C. A solution of maleic acid (13.2 g) in 2-butanol (120 mL) was added at a controlled rate over 1 hour below 5° C. When half of the maleic acid solution had been added, the mixture was seeded with 400 mg (1 wt %) of the maleate salt of compound (2a).

After complete addition of the maleic acid solution, the slurry was allowed to warm to ambient temperature. tent-Butyl methyl ether (60 mL) was added at a controlled rate over 1 hour, after which the slurry was aged at ambient temperature for an additional 3 hours. The crystalline product was then collected by filtration. The filter cake was washed twice with tert-butyl methyl ether (60 mL), after which the cake was dried under nitrogen flow-through. The maleate salt of compound (2a) (40.4 g, 71% yield) was obtained as an off-white powder.

Example 3 Preparation of a D-Malate Salt (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound 2(a)) Using a Transaminase Polypeptide of the Present Disclosure

The following example illustrates a method for preparing a D-malic acid salt of compound (2a), which can be used in the preparation of compound (3), in a biocatalytic reaction using an engineered polypeptide of the present disclosure.

The transaminase polypeptide of SEQ ID NO: 206 (1.25 g, 5 wt % relative to alkoxy ketone) and pyridoxal 5′-phosphate (250 mg, 1 wt %) were charged to a 3-neck RB flask. Borate buffer (0.2 M, 225 mL, 9 vol) with 1M iPrNH₂ at pH 10.5 was added. Dimethyl sulfoxide (12.5 mL, 0.5 vol) was added, and the resulting slurry was heated to 45° C. in a closed system. Once at 45° C., the pH of the slurry was adjusted to 10.5 using 4 M isopropylamine and a free standing titrating unit.

Compound (1) (26.6 g, 89 wt %, 85 mmol) was dissolved in dimethyl sulfoxide (12.5 mL, 0.5 vol). The compound (1) solution was added to the hot transaminase polypeptide slurry over 3 minutes. The resulting milky yellow slurry was aged 20 h while the pH was maintained at 10.5 by addition of isopropylamine (95% conversion by HPLC).

The mixture was then allowed to cool to ambient temperature, after which the slurry was extracted with a mixture of 107 mL tert-butyl methyl ether and 80 mL isopropanol. The aqueous phase was extracted with a mixture of 80 mL tert-butyl methyl ether and 53 mL isopropanol followed by the third extraction using 80 mL tert-butyl methyl ether and 40 mL isopropanol. The combined organic extracts (83% assay, 99.2:0.8 dr) were concentrated, diluted with isopropyl acetate (133 mL) and washed with 1 M K₃PO₄/KCl (133 mL). Organic layer was concentrated and diluted with isopropanol (67 mL).

A solution of D-(+)-malic acid (10.3 g, 77 mmol) in isopropanol (67 mL) was prepared. A 500 mL flask was charged with isopropanol (20 mL) and the D-malic acid salt of compound (2a) product (200 mg, 1.0 wt %) as seed. The resulting suspension was warmed to 35° C. The D-malic acid and primary amine solutions were added simultaneously to the suspension in the 500 mL flask. The slurry was allowed to stir to room temperature, filtered and the cake was washed with 1:2 isopropanol:tert-butyl methyl ether (90 mL) followed by tert-butyl methyl ether (90 mL). After drying under N₂, 28.35 g of white crystals of the compound (2a) product were obtained (80% isolated yield relative to compound (1), 99.95:0.05 dr, 99.8 A % by HPLC).

Example 4 Preparation of Compound (3) from a D-Malate Salt of Compound 2(a)

The following example illustrates a method for preparing compound (3) from the D-malate salt of compound (2a) (prepared as Example 3) via an N-hydroxysuccinimide intermediate.

A. Preparation of Hydroxysuccinimide of Compound (2a)

To a 50 mL 3-neck flask equipped with overhead stirring, a reflux condenser, a nitrogen inlet, and a thermocouple were added the D-malate salt of compound (2a) (3.00 g, 7.07 mmol), n-butylboronic acid (0.036 g, 0.353 mmol, 5 mol %), and n-propyl acetate (30.0 ml, 10 vol). The reaction was heated to reflux over 15 min (bath temperature 110° C.). After 7 hours, a distillation head was connected to the reaction flask. 15 mL of solvent was removed by distillation over 30 minutes to affect removal of water. The distillation head was then removed.

After an additional 3 hours, the temperature was set to 70° C. At this time HPLC analysis showed 96% conversion of the compound (2a) malate salt to a 7:1.5:1 mixture of the amido acids and the succinimide of compound (2a). Hexamethyldisilazane (2.95 ml, 14.13 mmol, 2.0 equiv) was added, followed by anhydrous zinc chloride (0.963 g, 7.07 mmol, 1.0 equiv). The temperature was maintained at 70° C. for 6 hours, after which HPLC analysis showed 98.2% conversion of the amides to the succinimide of compound (2a).

The mixture was then allowed to cool to 50° C. 1 M aqueous hydrochloric acid (15 mL, 5 vol) was added over 5 minutes, forming a clear biphasic solution. The phases were cut at 50° C. Subsequently, the organics were washed with additional 1 M aqueous hydrochloric acid (6 mL, 2 vol), with the cut again performed at 50° C. Total aqueous losses were 3.1%, and the assay yield of the succinimides of compound (2a) in the organics was 85%.

The organics were concentrated twice from n-propyl acetate (15 mL, 5 vol) to remove water. The resulting solid was suspended in n-propyl acetate to a total volume of 15 mL. The mixture was warmed to 60° C. to affect dissolution, then cooled to 45° C., at which point seed crystals (1 wt %) were added. The mixture was cooled to 22° C. over 3 hours. Heptane (18 mL, 6 vol) was added over 6 hours. The mixture was cooled to 2° C. over 4 hours, and the crystals were collected by filtration. The filter cake was washed with heptane (12 mL, 4 vol) and dried to constant weight by nitrogen flow through. 2.23 g (77% yield) of the hydroxysuccinimide of compound (2a) were obtained as white plates with 94 wt % purity and 94.9 LCAP. Combined liquor losses were 3.1%.

B. Preparation of Compound (3)

To a mixture of the compound (2a) hydroxysuccinimide (10.0 g) and sodium borohydride (2.89 g, 3.0 equiv) in tetrahydrofuran (50 mL, 5 vol) at 0° C. in a 200 mL 3-neck flask was added trimethylborate (B(OMe)₃, 2.8 mL, 1.0 equiv) over 5 min. After stirring at ambient temperature for 30 min, boron trifluoride etherate (BF3OEt2, 12.6 mL, 4.0 equiv) was added over 1 h at 0° C. This slurry was aged at ambient temperature for 2 h prior to heating at 40° C. for 17 h (˜99% cony already after 2 h at 40° C.).

The resulting slurry was then cooled to 0° C. and quenched with water (50 mL, 5 vol) below +10° C. This solution was then heated at 50° C. for 24 h (>99% cony). The resulting solution was diluted with iPrOAc (100 mL, 10 vol) and 28% aqueous ammonia (25 mL, 2.5 vol). After a 50° C. phase cut, the organic layer was washed with water (20 mL, 2 vol) and concentrated to 3 vol iPrOAc. iPrOH (30 mL, 3 vol) was added followed by 5 M HCl in iPrOH (4.1 mL, 1.0 equiv) over 1 h at 20° C. The resulting slurry was aged at room temperature for 14 h, cooled to 0° C. for 4 h and then filtered. Cake was washed with iPAc (50 mL, 5 vol) and dried under nitrogen to give 9.58 g of the HCl salt of compound (3) (98% yield, 99.5 A %).

All publications, patents, patent applications and other documents cited in this application are hereby incorporated by reference in their entireties for all purposes to the same extent as if each individual publication, patent, patent application or other document were individually indicated to be incorporated by reference for all purposes.

While various specific embodiments have been illustrated and described, it will be appreciated that various changes can be made without departing from the spirit and scope of the invention(s). 

What is claimed is:
 1. An engineered transaminase comprising an amino acid sequence having at least 90% sequence identity to the reference polypeptide of SEQ ID NO: 6 and an amino acid residue difference as compared to SEQ ID NO: 6 at the positions X69V, X124I, and X136W.
 2. The polypeptide of claim 1 in which the amino acid differences as compared to SEQ ID NO: 6 comprise X69V, X124I, and X136W.
 3. The polypeptide of claim 2 in which the polypeptide amino acid sequence further comprises one or more amino acid residue differences as compared to SEQ ID NO: 6 selected from the following: X2K; X2Q; X2S; X4I; X4L; X5H; X5I; X5L; X5N; X5S; X5T; X5V; X7A; X8T; X9N; X9Q; X9S; X10V; X11K; X14R; X28P; X37R; X38G; X41F; X42A; X44Q; X44V; X52K; X54K; X54N; X54P; X54R; X55L; X56G; X56L; X56S; X58L; X94L; X99L; X108V; X126A; X126T; X135Q; X141L; X142R; X142T; X150A; X150F; X150N; X155A; X156A; X156F; X156G; X156S; X156T; X157L; X164A; X165N; X171A; X182T; X199F; X199R; X199Y; X209C; X209D; X209E; X210S; X213P; X215F; X215Y; X217S; X218M; X22I; X223I; X223L; X223M; X223N; X245S; X257F; X265T; X267V; X296S; and X328I.
 4. The polypeptide of claim 1 in which the polypeptide is capable of converting a racemic mixture of compound (1) to compound (2a) in at least a 2:1 diastereomeric ratio relative to compound (2c) under suitable reaction conditions:


5. The polypeptide of claim 1 in which the polypeptide amino acid sequence comprises SEQ ID NO:206.
 6. A polynucleotide encoding the polypeptide of claim
 1. 7. An expression vector comprising the polynucleotide of claim
 6. 8. A host cell comprising the polynucleotide of claim
 6. 9. A method for preparing a polypeptide comprising culturing a host cell of claim 8 and isolating the polypeptide from the cell.
 10. A method for preparing (1R,2R)-2-(3,4-dimethoxyphenethoxy)cyclohexanamine (compound (2a)),

comprising contacting (R)-2-(3,4-dimethoxyphenethoxy)cyclohexanone (compound (1a))

with a transaminase polypeptide of claim 1 in the presence of an amino donor under suitable reactions conditions.
 11. The method of claim 10, wherein the suitable reaction conditions comprise at least about 10 g/L compound (1a), at least about 1 g/L polypeptide, at least about 1 M isopropylamine, at least about 1 g/L pyridoxal 5′-phosphate, 0.2 M borate, at least about 20% (v/v) DMSO, pH 10.5, and 45° C.
 12. The method of claim 10, in which the method further comprises one or more steps selected from: extraction of compound (2a); isolation of compound (2a); forming a salt of compound (2a); purification of compound (2a); and crystallization of compound (2a). 